1
|
Bergman M, Xiao X, Hall CK. In Silico Design and Analysis of Plastic-Binding Peptides. J Phys Chem B 2023; 127:8370-8381. [PMID: 37735840 PMCID: PMC10591858 DOI: 10.1021/acs.jpcb.3c04319] [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] [Indexed: 09/23/2023]
Abstract
Peptides that bind to inorganic materials can be used to functionalize surfaces, control crystallization, or assist in interfacial self-assembly. In the past, inorganic-binding peptides have been found predominantly through peptide library screening. While this method has successfully identified peptides that bind to a variety of materials, an alternative design approach that can intelligently search for peptides and provide physical insight for peptide affinity would be desirable. In this work, we develop a computational, physics-based approach to design inorganic-binding peptides, focusing on peptides that bind to the common plastics polyethylene, polypropylene, polystyrene, and poly(ethylene terephthalate). The PepBD algorithm, a Monte Carlo method that samples peptide sequence and conformational space, was modified to include simulated annealing, relax hydration constraints, and an ensemble of conformations to initiate design. These modifications led to the discovery of peptides with significantly better scores compared to those obtained using the original PepBD. PepBD scores were found to improve with increasing van der Waals interactions, although strengthening the intermolecular van der Waals interactions comes at the cost of introducing unfavorable electrostatic interactions. The best designs are enriched in amino acids with bulky side chains and possess hydrophobic and hydrophilic patches whose location depends on the adsorbed conformation. Future work will evaluate the top peptide designs in molecular dynamics simulations and experiment, enabling their application in microplastic pollution remediation and plastic-based biosensors.
Collapse
Affiliation(s)
- Michael Bergman
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27606, USA
| | - Xingqing Xiao
- Department of Chemistry, School of Science, Hainan University, Longhua District, Haikou, Hainan, 571101, China
| | - Carol K. Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27606, USA
| |
Collapse
|
2
|
Biomedical applications of solid-binding peptides and proteins. Mater Today Bio 2023; 19:100580. [PMID: 36846310 PMCID: PMC9950531 DOI: 10.1016/j.mtbio.2023.100580] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Over the past decades, solid-binding peptides (SBPs) have found multiple applications in materials science. In non-covalent surface modification strategies, solid-binding peptides are a simple and versatile tool for the immobilization of biomolecules on a vast variety of solid surfaces. Especially in physiological environments, SBPs can increase the biocompatibility of hybrid materials and offer tunable properties for the display of biomolecules with minimal impact on their functionality. All these features make SBPs attractive for the manufacturing of bioinspired materials in diagnostic and therapeutic applications. In particular, biomedical applications such as drug delivery, biosensing, and regenerative therapies have benefited from the introduction of SBPs. Here, we review recent literature on the use of solid-binding peptides and solid-binding proteins in biomedical applications. We focus on applications where modulating the interactions between solid materials and biomolecules is crucial. In this review, we describe solid-binding peptides and proteins, providing background on sequence design and binding mechanism. We then discuss their application on materials relevant for biomedicine (calcium phosphates, silicates, ice crystals, metals, plastics, and graphene). Although the limited characterization of SBPs still represents a challenge for their design and widespread application, our review shows that SBP-mediated bioconjugation can be easily introduced into complex designs and on nanomaterials with very different surface chemistries.
Collapse
|
3
|
Piletska E, Magumba K, Joseph L, Garcia Cruz A, Norman R, Singh R, Tabasso AFS, Jones DJL, Macip S, Piletsky S. Molecular imprinting as a tool for determining molecular markers: a lung cancer case. RSC Adv 2022; 12:17747-17754. [PMID: 35765329 PMCID: PMC9200412 DOI: 10.1039/d2ra01830f] [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: 03/21/2022] [Accepted: 05/23/2022] [Indexed: 11/29/2022] Open
Abstract
Determining which cancer patients will be sensitive to a given therapy is essential for personalised medicine. Thus, it is important to develop new tools that will allow us to stratify patients according to their predicted response to treatment. The aim of work presented here was to use molecular imprinting for determining the sensitivity of lung cancer cell lines to ionising radiation based on cell surface proteomic differences. Molecularly imprinted polymer nanoparticles (nanoMIPs) were formed in the presence of whole cells. Following trypsinolysis, protein epitopes protected by complexing with MIPs were eluted from the nanoparticles and analysed by LC-MS/MS. The analysis identified two membrane proteins, neutral amino acid transporter B (0) and 4F2 cell-surface antigen heavy chain, the abundance of which in the lung cancer cells could indicate resistance of these cells to radiotherapy. This proof-of-principle experiments shows that this technology can be used in the discovery of new biomarkers and in development of novel diagnostic and therapeutic tools for a personalised medicine approach to treating cancer. A first use of molecular imprinting for characterisation of surfaceome of the lung cancer cells and discovery of the molecular markers for radiosensitivity: towards development of an effective tool for cancer therapy and personalised medicine.![]()
Collapse
Affiliation(s)
- Elena Piletska
- School of Chemistry, College of Science and Engineering, University of Leicester Leicester UK +44-(0)116-0294-4666
| | - Kirabo Magumba
- School of Chemistry, College of Science and Engineering, University of Leicester Leicester UK +44-(0)116-0294-4666
| | - Lesslly Joseph
- School of Chemistry, College of Science and Engineering, University of Leicester Leicester UK +44-(0)116-0294-4666
| | - Alvaro Garcia Cruz
- School of Chemistry, College of Science and Engineering, University of Leicester Leicester UK +44-(0)116-0294-4666
| | - Rachel Norman
- Leicester Cancer Research Centre, University of Leicester Leicester Royal Infirmary Leicester UK
| | - Rajinder Singh
- Leicester Cancer Research Centre, University of Leicester Leicester Royal Infirmary Leicester UK
| | - Antonella F S Tabasso
- Leicester Cancer Research Centre, University of Leicester Leicester Royal Infirmary Leicester UK.,Mechanisms of Cancer and Ageing Laboratory, Department of Molecular and Cell Biology, University of Leicester Leicester UK
| | - Donald J L Jones
- Leicester Cancer Research Centre, University of Leicester Leicester Royal Infirmary Leicester UK.,Department of Cardiovascular Sciences, University of Leicester Leicester UK.,National Institute for Health Research, Leicester Biomedical Research Centre, Glenfield Hospital Leicester UK
| | - Salvador Macip
- Mechanisms of Cancer and Ageing Laboratory, Department of Molecular and Cell Biology, University of Leicester Leicester UK.,FoodLab, Faculty of Health Sciences, Universitat Oberta de Catalunya Barcelona Spain
| | - Sergey Piletsky
- School of Chemistry, College of Science and Engineering, University of Leicester Leicester UK +44-(0)116-0294-4666
| |
Collapse
|
4
|
Francino-Urdaniz IM, Whitehead TA. An overview of methods for the structural and functional mapping of epitopes recognized by anti-SARS-CoV-2 antibodies. RSC Chem Biol 2021; 2:1580-1589. [PMID: 34977572 PMCID: PMC8637828 DOI: 10.1039/d1cb00169h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 09/25/2021] [Indexed: 12/20/2022] Open
Abstract
This mini-review presents a critical survey of techniques used for epitope mapping on the SARS-CoV-2 Spike protein. The sequence and structures for common neutralizing and non-neutralizing epitopes on the Spike protein are described as determined by X-ray crystallography, electron microscopy and linear peptide epitope mapping, among other methods. An additional focus of this mini-review is an analytical appraisal of different deep mutational scanning workflows for conformational epitope mapping and identification of mutants on the Spike protein which escape antibody neutralization. Such a focus is necessary as a critical review of deep mutational scanning for conformational epitope mapping has not been published. A perspective is presented on the use of different epitope determination methods for development of broadly potent antibody therapies and vaccines against SARS-CoV-2.
Collapse
Affiliation(s)
- Irene M Francino-Urdaniz
- Department of Chemical and Biological Engineering, University of Colorado JSC Biotechnology Building, 3415 Colorado Avenue Boulder CO 80305 USA +1 303-735-2145
| | - Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado JSC Biotechnology Building, 3415 Colorado Avenue Boulder CO 80305 USA +1 303-735-2145
| |
Collapse
|
5
|
Peptide Affinity Chromatography Applied to Therapeutic Antibodies Purification. Int J Pept Res Ther 2021; 27:2905-2921. [PMID: 34690622 PMCID: PMC8525457 DOI: 10.1007/s10989-021-10299-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2021] [Indexed: 12/12/2022]
Abstract
The interest in therapeutic monoclonal antibodies (mAbs) has significantly grown in the pharmaceutical industry, exceeding 100 FDA mAbs approved. Although the upstream processing of their industrial production has been significantly improved in the last years, the downstream processing still depends on immobilized protein A affinity chromatography. The high cost, low capacity and short half-life of immobilized protein A chromatography matrices, encouraged the design of alternative short-peptide ligands for mAb purification. Most of these peptides have been obtained by screening combinatorial peptide libraries. These low-cost ligands can be easily produced by solid-phase peptide synthesis and can be immobilized on chromatographic supports, thus obtaining matrices with high capacity and selectivity. Furthermore, matrices with immobilized peptide ligands have longer half-life than those with protein A due to the higher stability of the peptides. In this review the design and synthesis of peptide ligands, their immobilization on chromatographic supports and the evaluation of the affinity supports for their application in mAb purification is described.
Collapse
|
6
|
Gopi C, Krupamai G, Sri CS, Dhanaraju MD. An overview of recent progress in modern synthetic approach—combinatorial synthesis. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2020. [DOI: 10.1186/s43088-020-00083-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
In recent times, a powerful tool of combinatorial synthesis has been used for the preparation of large chemical entities through a small set up of reactions between different building blocks using solid-phase and solution-phase techniques. This method reduced the time and cost of the drug discovery process substantially.
Main text
Thousands of compounds are synthesised in a few reactions through combinatorial synthesis instead of getting a few compounds in the traditional method. This method also helps to identify chemical lead of the compounds and optimise them through the biological screening using a high-throughput method. There is no review concerning the recent research finding of combinatorial synthesis. Hence, an attempt had been made on the latest research findings (2002–2020) of newly synthesised compounds using combinatorial synthesis and their biological activities.
Conclusion
To the best of our knowledge, the current review has completely analysed the importance of combinatorial synthesis and furnished an overview of solid-phase and solution-phase techniques as well as helped mankind by improving higher productivity at low cost, lead identification and optimization and preventing environmental pollution.
Graphical abstract
Collapse
|
7
|
Chu W, Prodromou R, Day KN, Schneible JD, Bacon KB, Bowen JD, Kilgore RE, Catella CM, Moore BD, Mabe MD, Alashoor K, Xu Y, Xiao Y, Menegatti S. Peptides and pseudopeptide ligands: a powerful toolbox for the affinity purification of current and next-generation biotherapeutics. J Chromatogr A 2020; 1635:461632. [PMID: 33333349 DOI: 10.1016/j.chroma.2020.461632] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 02/08/2023]
Abstract
Following the consolidation of therapeutic proteins in the fight against cancer, autoimmune, and neurodegenerative diseases, recent advancements in biochemistry and biotechnology have introduced a host of next-generation biotherapeutics, such as CRISPR-Cas nucleases, stem and car-T cells, and viral vectors for gene therapy. With these drugs entering the clinical pipeline, a new challenge lies ahead: how to manufacture large quantities of high-purity biotherapeutics that meet the growing demand by clinics and biotech companies worldwide. The protein ligands employed by the industry are inadequate to confront this challenge: while featuring high binding affinity and selectivity, these ligands require laborious engineering and expensive manufacturing, are prone to biochemical degradation, and pose safety concerns related to their bacterial origin. Peptides and pseudopeptides make excellent candidates to form a new cohort of ligands for the purification of next-generation biotherapeutics. Peptide-based ligands feature excellent target biorecognition, low or no toxicity and immunogenicity, and can be manufactured affordably at large scale. This work presents a comprehensive and systematic review of the literature on peptide-based ligands and their use in the affinity purification of established and upcoming biological drugs. A comparative analysis is first presented on peptide engineering principles, the development of ligands targeting different biomolecular targets, and the promises and challenges connected to the industrial implementation of peptide ligands. The reviewed literature is organized in (i) conventional (α-)peptides targeting antibodies and other therapeutic proteins, gene therapy products, and therapeutic cells; (ii) cyclic peptides and pseudo-peptides for protein purification and capture of viral and bacterial pathogens; and (iii) the forefront of peptide mimetics, such as β-/γ-peptides, peptoids, foldamers, and stimuli-responsive peptides for advanced processing of biologics.
Collapse
Affiliation(s)
- Wenning Chu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Raphael Prodromou
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kevin N Day
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - John D Schneible
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kaitlyn B Bacon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - John D Bowen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Ryan E Kilgore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Carly M Catella
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Brandyn D Moore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Matthew D Mabe
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kawthar Alashoor
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642
| | - Yiman Xu
- College of Material Science and Engineering, Donghua University, 201620 Shanghai, People's Republic of China
| | - Yuanxin Xiao
- College of Textile, Donghua University, Songjiang District, Shanghai, 201620, People's Republic of China
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606.
| |
Collapse
|
8
|
Ding Y, Vara Prasad CVNS, Wang B. Glycosylation on Unprotected or Partially Protected Acceptors. European J Org Chem 2020. [DOI: 10.1002/ejoc.201901675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yili Ding
- Life Science Department; Foshan University; 528000 Foshan Guangdong China
| | | | - Bingyun Wang
- Life Science Department; Foshan University; 528000 Foshan Guangdong China
| |
Collapse
|
9
|
Celasun S, Maron E, Börner HG. Peptide‐Assisted Design of Precision Polymer Sequences: On the Relevance of the Side‐Chain Sequences and the Variability of the Backbone. Macromol Biosci 2019; 20:e1900244. [DOI: 10.1002/mabi.201900244] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/09/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Sensu Celasun
- Laboratory for Organic Synthesis of Functional SystemsDepartment of ChemistryHumboldt‐Universität zu Berlin Brook‐Taylor‐Str. 2 12489 Berlin Germany
| | - Eva Maron
- Laboratory for Organic Synthesis of Functional SystemsDepartment of ChemistryHumboldt‐Universität zu Berlin Brook‐Taylor‐Str. 2 12489 Berlin Germany
| | - Hans G. Börner
- Laboratory for Organic Synthesis of Functional SystemsDepartment of ChemistryHumboldt‐Universität zu Berlin Brook‐Taylor‐Str. 2 12489 Berlin Germany
| |
Collapse
|
10
|
Li J, Carney RP, Liu R, Fan J, Zhao S, Chen Y, Lam KS, Pan T. Microfluidic Print-to-Synthesis Platform for Efficient Preparation and Screening of Combinatorial Peptide Microarrays. Anal Chem 2018; 90:5833-5840. [PMID: 29633611 DOI: 10.1021/acs.analchem.8b00371] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this paper, we introduce a novel microfluidic combinatorial synthesis platform, referred to as Microfluidic Print-to-Synthesis (MPS), for custom high-throughput and automated synthesis of a large number of unique peptides in a microarray format. The MPS method utilizes standard Fmoc chemistry to link amino acids on a polyethylene glycol (PEG)-functionalized microdisc array. The resulting peptide microarrays permit rapid screening for interactions with molecular targets or live cells, with low nonspecific binding. Such combinatorial peptide microarrays can be reliably prepared at a spot size of 200 μm with 1 mm center-to-center distance, dimensions that require only minimal reagent consumption (less than 30 nL per spot per coupling reaction). The MPS platform has a scalable design for extended multiplexibility, allowing for 12 different building blocks and coupling reagents to be dispensed in one microfluidic cartridge in the current format, and could be further scaled up. As proof of concept for the MPS platform, we designed and constructed a focused tetrapeptide library featuring 2560 synthetic peptide sequences, capped at the N-terminus with 4-[( N'-2-methylphenyl)ureido]phenylacetic acid. We then used live human T lymphocyte Jurkat cells as a probe to screen the peptide microarrays for their interaction with α4β1 integrin overexpressed and activated on these cells. Unlike the one-bead-one-compound approach that requires subsequent decoding of positive beads, each spot in the MPS array is spatially addressable. Therefore, this platform is an ideal tool for rapid optimization of lead compounds found in nature or discovered from diverse combinatorial libraries, using either biochemical or cell-based assays.
Collapse
Affiliation(s)
- Jiannan Li
- Department of Biomedical Engineering , University of California , Davis , California 95765 , United States
| | - Randy P Carney
- Department of Biochemistry and Molecular Medicine , University of California , Davis , California 95765 , United States
| | - Ruiwu Liu
- Department of Biochemistry and Molecular Medicine , University of California , Davis , California 95765 , United States
| | - Jinzhen Fan
- Department of Biomedical Engineering , University of California , Davis , California 95765 , United States
| | - Siwei Zhao
- Department of Biomedical Engineering , University of California , Davis , California 95765 , United States
| | - Yan Chen
- Shenzhen Institutes of Advanced Technology , Chinese Academy of Sciences , Shenzhen 518055 , People's Republic of China
| | - Kit S Lam
- Department of Biochemistry and Molecular Medicine , University of California , Davis , California 95765 , United States
| | - Tingrui Pan
- Department of Biomedical Engineering , University of California , Davis , California 95765 , United States
| |
Collapse
|
11
|
Affiliation(s)
- Lindsey C. Szymczak
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Hsin-Yu Kuo
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Milan Mrksich
- Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha 410082, China
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
12
|
ten Brummelhuis N, Wilke P, Börner HG. Identification of Functional Peptide Sequences to Lead the Design of Precision Polymers. Macromol Rapid Commun 2017; 38. [DOI: 10.1002/marc.201700632] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 09/26/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Niels ten Brummelhuis
- Laboratory for Organic Synthesis of Functional Systems; Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 D-12489 Berlin Germany
| | - Patrick Wilke
- Laboratory for Organic Synthesis of Functional Systems; Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 D-12489 Berlin Germany
| | - Hans G. Börner
- Laboratory for Organic Synthesis of Functional Systems; Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 D-12489 Berlin Germany
| |
Collapse
|
13
|
David A. Peptide ligand-modified nanomedicines for targeting cells at the tumor microenvironment. Adv Drug Deliv Rev 2017; 119:120-142. [PMID: 28506743 DOI: 10.1016/j.addr.2017.05.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/17/2017] [Accepted: 05/09/2017] [Indexed: 02/06/2023]
Abstract
Since their initial discovery more than 30years ago, tumor-homing peptides have become an increasingly useful tool for targeted delivery of therapeutic and diagnostic agents into tumors. Today, it is well accepted that cells at the tumor microenvironment (TME) contribute in many ways to cancer development and progression. Tumor-homing peptide-decorated nanomedicines can interact specifically with surface receptors expressed on cells in the TME, improve cellular uptake of nanomedicines by target cells, and impair tumor growth and progression. Moreover, peptide ligand-modified nanomedicines can potentially accumulate in the target tissue at higher concentrations than would small conjugates, thus increasing overall target tissue exposure to the therapeutic agent, enhance therapeutic efficacy and reduce side effects. This review describes the most studied peptide ligands aimed at targeting cells in the TME, discusses major obstacles and principles in the design of ligands for drug targeting and provides an overview of homing peptides in ligand-targeted nanomedicines that are currently in development for cancer therapy and diagnosis.
Collapse
Affiliation(s)
- Ayelet David
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel.
| |
Collapse
|
14
|
Singh J, Lopes D, Gomika Udugamasooriya D. Development of a large peptoid-DOTA combinatorial library. Biopolymers 2016; 106:673-84. [PMID: 27257968 PMCID: PMC5035194 DOI: 10.1002/bip.22883] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 04/15/2016] [Accepted: 05/31/2016] [Indexed: 01/03/2023]
Abstract
Conventional one-bead one-compound (OBOC) library synthesis is typically used to identify molecules with therapeutic value. The design and synthesis of OBOC libraries that contain molecules with imaging or even potentially therapeutic and diagnostic capacities (e.g. theranostic agents) has been overlooked. The development of a therapeutically active molecule with a built-in imaging component for a certain target is a daunting task, and structure-based rational design might not be the best approach. We hypothesize to develop a combinatorial library with potentially therapeutic and imaging components fused together in each molecule. Such molecules in the library can be used to screen, identify, and validate as direct theranostic candidates against targets of interest. As the first step in achieving that aim, we developed an on-bead library of 153,600 Peptoid-DOTA compounds in which the peptoids are the target-recognizing and potentially therapeutic components and the DOTA is the imaging component. We attached the DOTA scaffold to TentaGel beads using one of the four arms of DOTA, and we built a diversified 6-mer peptoid library on the remaining three arms. We evaluated both the synthesis and the mass spectrometric sequencing capacities of the test compounds and of the final library. The compounds displayed unique ionization patterns including direct breakages of the DOTA scaffold into two units, allowing clear decoding of the sequences. Our approach provides a facile synthesis method for the complete on-bead development of large peptidomimetic-DOTA libraries for screening against biological targets for the identification of potential theranostic agents in the future. © 2016 The Authors. Biopolymers Published by Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 673-684, 2016.
Collapse
Affiliation(s)
- Jaspal Singh
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX, 77204
| | - Daniel Lopes
- Advanced Imaging Research Center, UT-Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390
| | - D Gomika Udugamasooriya
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX, 77204.
- Department of Cancer Systems Imaging, MD Anderson Cancer Center, 1881 East Road, Houston, TX, 77030-4009.
- Advanced Imaging Research Center, UT-Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390.
- Department of Biochemistry, UT-Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390.
| |
Collapse
|
15
|
Gilad Y, Firer M, Gellerman G. Recent Innovations in Peptide Based Targeted Drug Delivery to Cancer Cells. Biomedicines 2016; 4:E11. [PMID: 28536378 PMCID: PMC5344250 DOI: 10.3390/biomedicines4020011] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 05/16/2016] [Accepted: 05/23/2016] [Indexed: 12/21/2022] Open
Abstract
Targeted delivery of chemotherapeutics and diagnostic agents conjugated to carrier ligands has made significant progress in recent years, both in regards to the structural design of the conjugates and their biological effectiveness. The goal of targeting specific cell surface receptors through structural compatibility has encouraged the use of peptides as highly specific carriers as short peptides are usually non-antigenic, are structurally simple and synthetically diverse. Recent years have seen many developments in the field of peptide based drug conjugates (PDCs), particularly for cancer therapy, as their use aims to bypass off-target side-effects, reducing the morbidity common to conventional chemotherapy. However, no PDCs have as yet obtained regulatory approval. In this review, we describe the evolution of the peptide-based strategy for targeted delivery of chemotherapeutics and discuss recent innovations in the arena that should lead in the near future to their clinical application.
Collapse
Affiliation(s)
- Yosi Gilad
- Department of Chemical Sciences, Ariel University, Ariel 40700, Israel.
- Department of Chemical Engineering and Biotechnology, Ariel University, Ariel 40700, Israel.
| | - Michael Firer
- Department of Chemical Engineering and Biotechnology, Ariel University, Ariel 40700, Israel.
| | - Gary Gellerman
- Department of Chemical Sciences, Ariel University, Ariel 40700, Israel.
| |
Collapse
|
16
|
Maaty WS, Weis DD. Label-Free, In-Solution Screening of Peptide Libraries for Binding to Protein Targets Using Hydrogen Exchange Mass Spectrometry. J Am Chem Soc 2016; 138:1335-43. [PMID: 26741284 DOI: 10.1021/jacs.5b11742] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
There is considerable interest in the discovery of peptide ligands that bind to protein targets. Discovery of such ligands is usually approached by screening large peptide libraries. However, the individual peptides must be tethered to a tag that preserves their individual identities (e.g., phage display or one-bead one-compound). To overcome this limitation, we have developed a method for screening libraries of label-free peptides for binding to a protein target in solution as a single batch. The screening is based on decreased amide hydrogen exchange by peptides that bind to the target. Hydrogen exchange is measured by mass spectrometry. We demonstrate the approach using a peptide library derived from the Escherichia coli proteome that contained 6664 identifiable features. The library was spiked separately with a peptide spanning the calmodulin binding domain of endothelial nitric oxide synthase (eNOS, 494-513) and a peptide spanning the N-terminal 20 residues of bovine ribonuclease A (S peptide). Human calmodulin and bovine ribonuclease S (RNase S) were screened against the library. Using a novel data analysis workflow, we identified the eNOS peptide as the only calmodulin binding peptide and S peptide as the only ribonuclease S binding peptide in the library.
Collapse
Affiliation(s)
- Walid S Maaty
- Department of Nucleic Acid and Protein Structure, Agricultural Genetic Engineering Research Institute, Agricultural Research Center , Giza 12619, Egypt
| | | |
Collapse
|
17
|
D’Hondt M, Bracke N, Taevernier L, Gevaert B, Verbeke F, Wynendaele E, De Spiegeleer B. Related impurities in peptide medicines. J Pharm Biomed Anal 2014; 101:2-30. [DOI: 10.1016/j.jpba.2014.06.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 06/05/2014] [Accepted: 06/08/2014] [Indexed: 12/16/2022]
|
18
|
Schussek S, Trieu A, Doolan DL. Genome- and proteome-wide screening strategies for antigen discovery and immunogen design. Biotechnol Adv 2014; 32:403-14. [DOI: 10.1016/j.biotechadv.2013.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 11/04/2013] [Accepted: 12/16/2013] [Indexed: 01/17/2023]
|
19
|
Affiliation(s)
- Bethany Powell Gray
- Department of Internal Medicine and The Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8807, United States
| | - Kathlynn C. Brown
- Department of Internal Medicine and The Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8807, United States
| |
Collapse
|
20
|
Konieczna I, Zarnowiec P, Kwinkowski M, Kolesinska B, Fraczyk J, Kaminski Z, Kaca W. Bacterial urease and its role in long-lasting human diseases. Curr Protein Pept Sci 2013; 13:789-806. [PMID: 23305365 PMCID: PMC3816311 DOI: 10.2174/138920312804871094] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 07/15/2012] [Accepted: 09/03/2012] [Indexed: 02/07/2023]
Abstract
Urease is a virulence factor found in various pathogenic bacteria. It is essential in colonization of a host organism and in maintenance of bacterial cells in tissues. Due to its enzymatic activity, urease has a toxic effect on human cells. The presence of ureolytic activity is an important marker of a number of bacterial infections. Urease is also an immunogenic protein and is recognized by antibodies present in human sera. The presence of such antibodies is connected with progress of several long-lasting diseases, like rheumatoid arthritis, atherosclerosis or urinary tract infections. In bacterial ureases, motives with a sequence and/or structure similar to human proteins may occur. This phenomenon, known as molecular mimicry, leads to the appearance of autoantibodies, which take part in host molecules destruction. Detection of antibodies-binding motives (epitopes) in bacterial proteins is a complex process. However, organic chemistry tools, such as synthetic peptide libraries, are helpful in both, epitope mapping as well as in serologic investigations. In this review, we present a synthetic report on a molecular organization of bacterial ureases - genetic as well as structural. We characterize methods used in detecting urease and ureolytic activity, including techniques applied in disease diagnostic processes and in chemical synthesis of urease epitopes. The review also provides a summary of knowledge about a toxic effect of bacterial ureases on human body and about occurrence of anti-urease antibodies in long-lasting diseases.
Collapse
Affiliation(s)
- Iwona Konieczna
- Department of Microbiology, Institute of Biology, The Jan Kochanowski University, ul. Swietokrzyska 15, 25-406 Kielce, Poland.
| | | | | | | | | | | | | |
Collapse
|
21
|
Sensing Immune Responses with Customized Peptide Microarrays. Biointerphases 2012; 7:47. [DOI: 10.1007/s13758-012-0047-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 07/13/2012] [Indexed: 11/25/2022] Open
|
22
|
Increased affinity and solubility of peptides used for direct peptide ELISA on polystyrene surfaces through fusion with a polystyrene-binding peptide tag. Biotechniques 2012; 52:95-102. [PMID: 22313407 DOI: 10.2144/000113810] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 12/19/2011] [Indexed: 11/23/2022] Open
Abstract
Peptide reagents can serve as alternatives or replacements to antibodies in sensing or diagnostic applications. The passive adsorption of peptides onto polystyrene surfaces can limit the target binding capability, especially for short, positively charged, or hydrophobic sequences. In this report, we show that fusing a peptide with a previously characterized 12-amino acid polystyrene binding sequence (PS-tag) improves overall peptide solubility and enzyme-linked immunosorbent assay (ELISA) results using the peptide as a capture agent. Specific improvements for protective antigen (PA; Bacillus anthracis) protein binding peptides selected from bacterial surface display were compared with native or biotinylated peptides. The PS-tag was added to either peptide terminus, using a (Gly)(4) spacer, and comparable binding affinities were obtained. Fusion with the PS-tag did not have any negative impact on peptide secondary structure as measured by circular dichroism. The addition of the PS-tag provides a convenient method to utilize peptide reagents from peptide display libraries as capture agents in an ELISA format without the need for a biotin tag or concerns about passive adsorption of critical residues for target capture.
Collapse
|
23
|
Bédard F, Girard A, Biron É. A Convenient Approach to Prepare Topologically Segregated Bilayer Beads for One-Bead Two-Compound Combinatorial Peptide Libraries. Int J Pept Res Ther 2012. [DOI: 10.1007/s10989-012-9316-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
24
|
Kroening K, Johnston SA, Legutki JB. Autoreactive antibodies raised by self derived de novo peptides can identify unrelated antigens on protein microarrays. Are autoantibodies really autoantibodies? Exp Mol Pathol 2012; 92:304-11. [DOI: 10.1016/j.yexmp.2012.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 03/01/2012] [Indexed: 10/28/2022]
|
25
|
Bi J, Song R, Yang H, Li B, Fan J, Liu Z, Long C. Stepwise identification of HLA-A*0201-restricted CD8+ T-cell epitope peptides from herpes simplex virus type 1 genome boosted by a StepRank scheme. Biopolymers 2011; 96:328-39. [PMID: 21072852 DOI: 10.1002/bip.21564] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Identification of immunodominant epitopes is the first step in the rational design of peptide vaccines aimed at T-cell immunity. To date, however, it is yet a great challenge for accurately predicting the potent epitope peptides from a pool of large-scale candidates with an efficient manner. In this study, a method that we named StepRank has been developed for the reliable and rapid prediction of binding capabilities/affinities between proteins and genome-wide peptides. In this procedure, instead of single strategy used in most traditional epitope identification algorithms, four steps with different purposes and thus different computational demands are employed in turn to screen the large-scale peptide candidates that are normally generated from, for example, pathogenic genome. The steps 1 and 2 aim at qualitative exclusion of typical nonbinders by using empirical rule and linear statistical approach, while the steps 3 and 4 focus on quantitative examination and prediction of the interaction energy profile and binding affinity of peptide to target protein via quantitative structure-activity relationship (QSAR) and structure-based free energy analysis. We exemplify this method through its application to binding predictions of the peptide segments derived from the 76 known open-reading frames (ORFs) of herpes simplex virus type 1 (HSV-1) genome with or without affinity to human major histocompatibility complex class I (MHC I) molecule HLA-A*0201, and find that the predictive results are well compatible with the classical anchor residue theory and perfectly match for the extended motif pattern of MHC I-binding peptides. The putative epitopes are further confirmed by comparisons with 11 experimentally measured HLA-A*0201-restrcited peptides from the HSV-1 glycoproteins D and K. We expect that this well-designed scheme can be applied in the computational screening of other viral genomes as well.
Collapse
Affiliation(s)
- Jianjun Bi
- Department of Dermatology, General Hospital of Guangzhou Military Command of PLA, Guangzhou, China
| | | | | | | | | | | | | |
Collapse
|
26
|
Katz C, Levy-Beladev L, Rotem-Bamberger S, Rito T, Rüdiger SGD, Friedler A. Studying protein–protein interactions using peptide arrays. Chem Soc Rev 2011; 40:2131-45. [DOI: 10.1039/c0cs00029a] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
27
|
Townsend JB, Shaheen F, Liu R, Lam KS. Jeffamine derivatized TentaGel beads and poly(dimethylsiloxane) microbead cassettes for ultrahigh-throughput in situ releasable solution-phase cell-based screening of one-bead-one-compound combinatorial small molecule libraries. ACTA ACUST UNITED AC 2010; 12:700-12. [PMID: 20593859 DOI: 10.1021/cc100083f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A method to efficiently immobilize and partition large quantities of microbeads in an array format in microfabricated poly(dimethylsiloxane) (PDMS) cassette for ultrahigh-throughput in situ releasable solution-phase cell-based screening of one-bead-one-compound (OBOC) combinatorial libraries is described. Commercially available Jeffamine triamine T-403 (∼440 Da) was derivatized such that two of its amino groups were protected by Fmoc and the remaining amino group capped with succinic anhydride to generate a carboxyl group. This resulting trifunctional hydrophilic polymer was then sequentially coupled two times to the outer layer of topologically segregated bilayer TentaGel (TG) beads with solid phase peptide synthesis chemistry resulting in beads with increased loading capacity, hydrophilicity, and porosity at the outer layer. We have found that such bead configuration can facilitate ultrahigh-throughput in situ releasable solution-phase screening of OBOC libraries. An encoded releasable OBOC small molecule library was constructed on Jeffamine derivatized TG beads with library compounds tethered to the outer layer via a disulfide linker and coding tags in the interior of the beads. Compound-beads could be efficiently loaded (5-10 min) into a 5 cm diameter Petri dish containing a 10,000-well PDMS microbead cassette, such that over 90% of the microwells were each filled with only one compound-bead. Jurkat T-lymphoid cancer cells suspended in Matrigel were then layered over the microbead cassette to immobilize the compound-beads. After 24 h of incubation at 37 °C, dithiothreitol was added to trigger the release of library compounds. Forty-eight hours later, MTT reporter assay was used to identify regions of reduced cell viability surrounding each positive bead. From a total of about 20,000 beads screened, 3 positive beads were detected and physically isolated for decoding. A strong consensus motif was identified for these three positive compounds. These compounds were resynthesized and found to be cytotoxic (IC(50) 50-150 μM) against two T-lymphoma cell lines and less so against the MDA-MB 231 breast cancer cell line. This novel ultrahigh-throughput OBOC releasable method can potentially be adapted to many existing 96- or 384-well solution-phase cell-based or biochemical assays.
Collapse
Affiliation(s)
- Jared B Townsend
- Department of Biochemistry and Molecular Medicine, Division of Hematology & Oncology, University of California Davis Cancer Center, University of California Davis, 4501 X Street, Sacramento, California 95817, USA
| | | | | | | |
Collapse
|
28
|
Ho IAW, Hui KM, Lam PYP. Isolation of peptide ligands that interact specifically with human glioma cells. Peptides 2010; 31:644-50. [PMID: 20026365 DOI: 10.1016/j.peptides.2009.12.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 12/14/2009] [Accepted: 12/14/2009] [Indexed: 10/20/2022]
Abstract
Poor prognosis of high grade gliomas coupled with the difficulty of widespread delivery of therapeutic agents prompted the search into new molecular targets. Our aim is to isolate glioma-specific peptide sequences that can be used for targeted delivery of therapeutic drugs and imaging tracer to accurately demarcate tumor volume as a response to therapy. Herein, we describe the isolation and characterization of a glioma-specific peptide sequence, GL1, that interact exclusively with human glioma cells lines and primary glioma cells derived from human biopsy in vitro. Further analysis showed that the receptors for GL1 were located on the external side of the plasma membrane, where the GL1 peptides could bind stably up to a period of 180 min. More importantly, GL1 phages home specifically to human glioma xenograft when administered through tail vein, a phenomenon that was not observed when non-specific phages were used as control. Taken together, our results confirmed that GL1 could represent a novel peptide that target to tumor of glial origins, and could potentially be used as a targeting moiety for the conjugation of therapeutic drugs or diagnostic imaging radiolabels.
Collapse
Affiliation(s)
- Ivy A W Ho
- Laboratory of Cancer Gene Therapy, Singapore
| | | | | |
Collapse
|
29
|
Breitling F, Felgenhauer T, Nesterov A, Lindenstruth V, Stadler V, Bischoff FR. Particle-based synthesis of peptide arrays. Chembiochem 2009; 10:803-8. [PMID: 19191248 DOI: 10.1002/cbic.200800735] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Lithographic methods allow for the combinatorial synthesis of >50,000 oligonucleotides per cm(2), and this has revolutionized the field of genomics. High-density peptide arrays promise to advance the field of proteomics in a similar way, but currently lag behind. This is mainly due to the monomer-by-monomer repeated consecutive coupling of 20 different amino acids associated with lithography, which adds up to an excessive number of coupling cycles. Combinatorial synthesis based on electrically charged solid amino acid particles resolves this problem. A color laser printer or a chip addresses the different charged particles consecutively to a solid support, where, when completed, the whole layer of solid amino acid particles is melted at once. This frees hitherto immobilized amino acids to couple all 20 different amino acids to the support in one single coupling reaction. The method should allow for the translation of entire genomes into sets of overlapping peptides to be used in proteome research.
Collapse
Affiliation(s)
- Frank Breitling
- Department of Chip-Based Peptide Arrays, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.
| | | | | | | | | | | |
Collapse
|
30
|
Marani MM, Martínez Ceron MC, Giudicessi SL, de Oliveira E, Côté S, Erra-Balsells R, Albericio F, Cascone O, Camperi SA. Screening of one-bead-one-peptide combinatorial library using red fluorescent dyes. Presence of positive and false positive beads. ACTA ACUST UNITED AC 2009; 11:146-50. [PMID: 19072229 DOI: 10.1021/cc800145c] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To screen one-bead-one-compound (OBOC) combinatorial libraries, tens of thousands to millions of compound beads are first mixed with a target molecule. The beads that interact with this molecule are then identified and isolated for compound structure determination. Here we describe an OBOC peptide library screening using streptavidin (SA) as probe protein, labeled with a red fluorescent dye and using the COPAS BIO-BEAD flow sorting equipment to separate fluorescent from nonfluorescent beads. The red dyes used were ATTO 590 and Texas Red. After incubating the library with the SA-red fluorescent dye conjugate, we isolated positive beads caused by peptide-SA interaction and false positive beads produced by peptide fluorescent dye interaction. These false positives were a drawback when sorting beads by COPAS. However,an in depth analysis of both kinds of beads allowed the differentiation of positives from false positives. The false positive beads showed bright homogeneous fluorescence, while positive beads had a heterogeneous fluorescence, exhibiting a characteristic halo appearance, with fluorescence intensity greatest at the bead surface and lowest in the core. The difference was more evident when using Texas Red instead of ATTO 590. Thus, positive beads could be manually separated from false positive ones. The beads were analyzed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Most of the sequences obtained from positive beads had the His-Pro-Gln motif. Peptides from false positive beads were rich in Leu/Ileu, His, Phe, and Tyr.
Collapse
Affiliation(s)
- Mariela M Marani
- Cátedra de Microbiología Industrial y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Identification of novel peptides specifically binding to endometriosis by screening phage-displaying peptide libraries. Fertil Steril 2009; 92:1850-5. [PMID: 19200967 DOI: 10.1016/j.fertnstert.2008.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2007] [Revised: 08/24/2008] [Accepted: 09/03/2008] [Indexed: 01/18/2023]
Abstract
OBJECTIVE To search for novel peptides and common binding motif that specifically bind to endometriosis. DESIGN Prospective study. SETTING Department of Biological Science and Technology in national university. PATIENT(S) Specimens were divided into [1] ectopic endometrium (n = 10); [2] eutopic endometrium (n = 10). INTERVENTION(S) Peptides specifically binding to endometriosis are screened from a phage-displaying peptide library (Ph.D.-12) by using whole-cell screening technique after an adsorption elution amplification procedure. MAIN OUTCOME MEASURE(S) Combinatorial peptide libraries were used to identify small molecules that bind with high affinity to receptor molecules and mimic the interaction with natural ligands. Few pans of positive phage clones with significantly positive signals were identified by ELISA and analyzed by DNA sequencing. RESULT(S) During the biopanning processes, the recovered phage number (10(6) pfu/mL) in parts 1, 2, 3, 4, and 5 of the study were 9, 33, 82, 142, and 169. Nine phages consistently had residue Arg, whereas six clones had a consensus motif of Arg-X-Arg-X-X-X-X-Arg. The biotin-labeled peptide bound to endometriosis cells in a dose-dependent manner, yet the control peptide revealed lesser binding activity. CONCLUSION(S) The novel motif is associated with higher affinity of endometriosis, which might be useful in endometriosis targeting and as potential antiendometriosis therapies. We provide one potential approach for novel therapies toward endometriosis.
Collapse
|
32
|
Breitling F, Nesterov A, Stadler V, Felgenhauer T, Bischoff FR. High-density peptide arrays. MOLECULAR BIOSYSTEMS 2009; 5:224-34. [PMID: 19225611 DOI: 10.1039/b819850k] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Arrays promise to advance biology by allowing parallel screening for many different binding partners. Meanwhile, lithographic methods enable combinatorial synthesis of > 50,000 oligonucleotides per cm(2), an advance that has revolutionized the whole field of genomics. A similar development is expected for the field of proteomics, provided that affordable, very high-density peptide arrays are available. However, peptide arrays lag behind oligonucleotide arrays. This review discusses recent developments in the field with an emphasis on methods that lead to very high-density peptide arrays.
Collapse
Affiliation(s)
- Frank Breitling
- German Cancer Research Center, Im Neuenheimer Feld 580, Heidelberg, Germany.
| | | | | | | | | |
Collapse
|
33
|
Abstract
Advances in the engineering of peptides, adjuvants and delivery systems have renewed the enthusiasm for peptide-based vaccination regimens in the setting of cancer, and there are a variety of clinical trials being conducted by pharmaceutical companies based on the use of peptides. The challenges to successful cancer immunotherapy are common to all immunotherapeutic strategies and not unique to peptide-based vaccination regimens. This review will describe the advances in the identification, design and delivery of peptides, the challenges to successful immunotherapy and will discuss potential options for the future.
Collapse
Affiliation(s)
- Shreya Kanodia
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center, NRT 7517, University of Southern California, 1450 Biggy Street, Los Angeles, CA 90033, USA.
| | | |
Collapse
|
34
|
Aina OH, Liu R, Sutcliffe JL, Marik J, Pan CX, Lam KS. From Combinatorial Chemistry to Cancer-Targeting Peptides. Mol Pharm 2007; 4:631-51. [PMID: 17880166 DOI: 10.1021/mp700073y] [Citation(s) in RCA: 220] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Several monoclonal antibodies that target cell surface receptors have gained approval by the U.S. Food and Drug Administration and are widely used in the treatment of some cancers. These include but are not limited to the anti-CD20 antibody Rituximab, used in lymphoma treatment, as well as anti-HER-2 antibody for breast cancer therapy. The efficacy of this cancer immunotherapy modality is, however, limited by the large size of the antibody (160 kd) and its relatively nonspecific binding to the reticuloendothelial system. This latter property is particularly problematic if the antibody is used as a vehicle to deliver radionuclides, cytotoxic drugs, or toxins to the tumor site. Peptides, peptidomimetic, or small molecules are thus attractive as alternative cell surface targeting agents for cancer imaging and therapy. Cancer cell surface targeting peptides can be derived from known native peptide hormones such as somatostatin and bombesin, or they can be identified through screening combinatorial peptide libraries against unknown cell surface receptor targets. Phage-display peptide library and one-bead one-compound (OBOC) combinatorial library methods have been successfully used to discover peptides that target cancer cells or tumor blood vessel endothelial cells. The phage-display peptide library method, because of its biological nature, can only display l-amino acid peptides. In contrast, the OBOC combinatorial library method allows for bead-surface display of peptides that contain l-amino acids, d-amino acids, unnatural amino acids, or other organic moieties. We have successfully used the OBOC method to discover and optimize ligands against unique cell surface receptors of prostate cancer, T- and B-cell lymphoma, as well as ovarian and lung cancers, and we have used some of these peptides to image xenografts in nude mice with high specificity. Here, we (i) review the literature on the use of phage-display and OBOC combinatorial library methods to discover cancer and tumor blood vessel targeting ligands, and (ii) report on the use of an ovarian cancer targeting ligand, OA02, as an in vivo PET imaging probe in a xenograft model in nude mice.
Collapse
Affiliation(s)
- Olulanu H Aina
- U.C. Davis Cancer Center, Division of Hematology/Oncology, Department of Internal Medicine, University of California-Davis, 4501 X Street, Sacramento, CA 95817, USA
| | | | | | | | | | | |
Collapse
|
35
|
Ding H, Prodinger WM, Kopeèek J. Two-step fluorescence screening of CD21-binding peptides with one-bead one-compound library and investigation of binding properties of N-(2-hydroxypropyl)methacrylamide copolymer-peptide conjugates. Biomacromolecules 2007; 7:3037-46. [PMID: 17096529 PMCID: PMC2536624 DOI: 10.1021/bm060508f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Using the one-bead one-compound (OBOC) combinatorial method, four heptapeptide ligands of CD21 receptor, a cell surface marker of malignant B cell lymphoma, were identified with an innovative two-step fluorescence screening method to overcome the limitation caused by autofluorescence of TentaGel resin. The binding affinities of selected peptides, YILIHRN (B1), PTLDPLP (B2), and LVLLTRE (B3), were in the micromolar region as determined by a fluorescence quenching assay. Peptide B1 was conjugated to N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer via spacers of different lengths, composed of one to four repeats of the 8-amino-3,6-dioxaoctanoic acid (A) group. The evaluation of the biorecognizability of HPMA copolymer-B1 conjugates by the CD21 receptor revealed that increasing the number of repeats of A in the spacer from one to three resulted in continuous improvements in the biorecognition by the CD21 receptor; the increase from three to four repeats showed no significant effect. This work showed the potential of the OBOC combinatorial approach to select peptide ligands as targeting moieties for CD21 specific polymeric drug carriers.
Collapse
Affiliation(s)
| | | | - Jindøich Kopeèek
- *To whom correspondence should be addressed. Phone: (801) 581-7211. Fax: (801) 581-7848. E-mail:
| |
Collapse
|
36
|
Cruz DJM, Kim CJ, Shin HJ. Phage-displayed peptides having antigenic similarities with porcine epidemic diarrhea virus (PEDV) neutralizing epitopes. Virology 2006; 354:28-34. [PMID: 16950494 PMCID: PMC7111992 DOI: 10.1016/j.virol.2006.04.027] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Revised: 02/21/2006] [Accepted: 04/21/2006] [Indexed: 11/17/2022]
Abstract
Seven-mer phage random peptide libraries were panned against 2C10, a monoclonal antibody that showed neutralizing activities against PEDV. Recombinant M13 phages displaying the peptides SHRLP(Y/Q)(P/V) or GPRPVTH on the g3p minor coat protein showed strong binding affinity with 2C10 (70% and 30% of recovered phages, respectively) after multiple panning. Sequence analysis suggested that these peptides are similar with (1368)GPRLQPY(1374) found at the carboxy-terminal of the S protein. In neutralization inhibition assays, the two peptide motifs and a 24-mer synthetic peptide corresponding to the C-terminal endodomain of PEDV S protein were observed to compete for the antigen binding site of 2C10, as demonstrated by the loss or reduction of neutralizing activity of the monoclonal antibody. This new finding suggests that the newly discovered peptide motifs mimic a neutralizing epitope PEDV.
Collapse
Affiliation(s)
- Deu John M Cruz
- #303 Animal Hospital, College of Veterinary Medicine, Chungnam National University, 220 Gungdong, Yuseong, Deajeon City, 305-764 Republic of Korea
| | | | | |
Collapse
|
37
|
Moore GJ, Moore DM, Roy SS, Hayden LJ, Hamilton MG, Chan NWC, Lee WE. Hinge peptide combinatorial libraries for inhilbitors of botulinum neurotoxins and saxitoxin: Deconvolution strategy. Mol Divers 2006; 10:9-16. [PMID: 16404524 DOI: 10.1007/s11030-006-1394-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Accepted: 07/27/2005] [Indexed: 10/25/2022]
Abstract
Abstract Combinatorial library screening offers a rapid process for identifying potential therapies to toxins. Hinge peptide libraries, which rely on conformational diversity rather than traditional molecular diversity, reduce the need for huge numbers of syntheses and screening steps and greatly expedite the discovery process of active molecules. Hinge peptide libraries having the structures: Acetyl-X1-X2-hinge-X3-X4-NH2 (capped) and X1-hinge-X2-X3 (uncapped), where X1 through X4 are near-equimolar mixtures of twelve L-amino acids and hinge = 4-aminobutyric acid, were screened for inhibitory activity in bioassays for botulinum neurotoxins A and B (BoNT/A, BoNT/B) and saxitoxin. The zinc protease activity of the reduced light chains of BoNT/A and /B was assayed by measuring the cleavage of synthetic substrates. Saxitoxin activity was measured by the restoration of the viability of neuroblastoma cells treated with ouabain and veratridine. Deconvolution of libraries was accomplished by fixing one position at a time beginning with the C-terminus. Primary library subsets in which position 4 was fixed showed moderate levels of inhibition for BoNT/A. Secondary library subsets showed stronger inhibition in the bioassays. In each of the bioassays, inhibitory potency was stronger when the second position to be fixed was on the opposite side of the hinge, rather than on the same side with respect to the C-terminus, suggesting that the hinge facilitates the interaction of side chains. Inhibitors for all three of the toxins studied were discovered within library subsets, although not necessarily in primary subsets. These studies demonstrate that (1) the best strategy for deconvoluting hinge peptide libraries is by fixing residues alternately on each side of the hinge moiety, and (2) it is essential to investigate secondary subsets even when primary subsets are inactive. The present findings support the concept that the increased flexibility imposed by the inclusion of a central hinge residue in small peptides increases the opportunity for side chain interactions, providing a distinct advantage for hinge peptide libraries over conventional peptide libraries. Hinge peptide libraries are a rich source of novel ligands for modulation of biomechanisms. The library subsets uncovered in this study may possess peptides that will lead to effective therapies to neurotoxin poisoning.
Collapse
Affiliation(s)
- Graham J Moore
- PepMetics Inc., 772 Murphy Place, Victoria, British Columbia, Canada V8Y 3H4
| | | | | | | | | | | | | |
Collapse
|
38
|
Toseland CP, Clayton DJ, McSparron H, Hemsley SL, Blythe MJ, Paine K, Doytchinova IA, Guan P, Hattotuwagama CK, Flower DR. AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data. Immunome Res 2005; 1:4. [PMID: 16305757 PMCID: PMC1289288 DOI: 10.1186/1745-7580-1-4] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2005] [Accepted: 10/06/2005] [Indexed: 11/30/2022] Open
Abstract
AntiJen is a database system focused on the integration of kinetic, thermodynamic, functional, and cellular data within the context of immunology and vaccinology. Compared to its progenitor JenPep, the interface has been completely rewritten and redesigned and now offers a wider variety of search methods, including a nucleotide and a peptide BLAST search. In terms of data archived, AntiJen has a richer and more complete breadth, depth, and scope, and this has seen the database increase to over 31,000 entries. AntiJen provides the most complete and up-to-date dataset of its kind. While AntiJen v2.0 retains a focus on both T cell and B cell epitopes, its greatest novelty is the archiving of continuous quantitative data on a variety of immunological molecular interactions. This includes thermodynamic and kinetic measures of peptide binding to TAP and the Major Histocompatibility Complex (MHC), peptide-MHC complexes binding to T cell receptors, antibodies binding to protein antigens and general immunological protein-protein interactions. The database also contains quantitative specificity data from position-specific peptide libraries and biophysical data, in the form of diffusion co-efficients and cell surface copy numbers, on MHCs and other immunological molecules. The uses of AntiJen include the design of vaccines and diagnostics, such as tetramers, and other laboratory reagents, as well as helping parameterize the bioinformatic or mathematical in silico modeling of the immune system. The database is accessible from the URL: .
Collapse
Affiliation(s)
- Christopher P Toseland
- Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK
| | - Debra J Clayton
- Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK
| | - Helen McSparron
- Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK
| | - Shelley L Hemsley
- Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK
| | - Martin J Blythe
- Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK
| | - Kelly Paine
- Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK
| | - Irini A Doytchinova
- Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK
| | - Pingping Guan
- Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK
| | - Channa K Hattotuwagama
- Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK
| | - Darren R Flower
- Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK
| |
Collapse
|
39
|
Hardy B, Raiter A. A mimotope peptide-based anti-cancer vaccine selected by BAT monoclonal antibody. Vaccine 2005; 23:4283-91. [PMID: 15919139 DOI: 10.1016/j.vaccine.2005.04.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2004] [Revised: 01/19/2005] [Accepted: 04/13/2005] [Indexed: 02/07/2023]
Abstract
Combinatorial phage display peptide libraries are employed to identify small molecules which bind with high affinity to receptor molecules and which mimic the interaction with natural ligands. We used a synthetic combinatory phage display peptide library to screen for peptides that bind BAT monoclonal antibody, an immune modulatory and anti-tumor antibody, to serve as the basis for an anti-cancer vaccine. Two distinct mimotopes, peptides A and B, were isolated, with repeated Proline, Arginine, and Isoleucine amino acids. Mimotope binding was determined by direct binding and by inhibition of BAT binding to the peptide bound phages and to Daudi cells. Immunization of mice with the peptides induced cellular and humoral responses. Cellular response was manifested by significant increase in cytolitic activity. Humoral response was manifested by production of specific antibodies. Serum purified IgG fraction contained anti-peptide antibodies that identified BAT binding mimotopes and competed with BAT binding on Daudi cells. These "BAT like" antibodies exhibited similar immune stimulatory properties to BAT. Immunization of mice with the peptides prevented tumor growth. These finding are the basis for the development of an anti-cancer vaccine.
Collapse
Affiliation(s)
- Britta Hardy
- Felsenstein Medical Research Center, Tel Aviv University School of Medicine, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel.
| | | |
Collapse
|
40
|
Liang F, Feng XJ, Lowry M, Rabitz H. Maximal Use of Minimal Libraries through the Adaptive Substituent Reordering Algorithm. J Phys Chem B 2005; 109:5842-54. [PMID: 16851637 DOI: 10.1021/jp045926y] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper describes an adaptive algorithm for interpolation over a library of molecules subjected to synthesis and property assaying. Starting with a coarse sampling of the library compounds, the algorithm finds the optimal substituent orderings on all of the functionalized scaffold sites to allow for accurate property interpolation over all remaining compounds in the full library space. A previous paper introduced the concept of substituent reordering and a smoothness-based criterion to search for optimal orderings (Shenvi, N.; Geremia, J. M.; Rabitz, H. J. Phys. Chem. A 2003, 107, 2066). Here, we propose a data-driven root-mean-squared (RMS) criteria and a combined RMS/smoothness criteria as alternative methods for the discovery of optimal substituent orderings. Error propagation from the property measurements of the sampled compounds is determined to provide confidence intervals on the interpolated molecular property values, and a substituent rescaling technique is introduced to manage poorly designed/sampled libraries. Finally, various factors are explored that can influence the applicability and interpolation quality of the algorithm. An adaptive methodology is proposed to iteratively and efficiently use laboratory experiments to optimize these algorithmic factors, so that the accuracy of property predictions is maximized. The enhanced algorithm is tested on copolymer and transition metal complex libraries, and the results demonstrate the capability of the algorithm to accurately interpolate various properties of both molecular libraries.
Collapse
Affiliation(s)
- Fan Liang
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | | | | | | |
Collapse
|
41
|
Ho IAW, Lam PYP, Hui KM. Identification and characterization of novel human glioma-specific peptides to potentiate tumor-specific gene delivery. Hum Gene Ther 2005; 15:719-32. [PMID: 15319030 DOI: 10.1089/1043034041648372] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Glioblastomas account for approximately 20% of all primary brain tumors in adults. Glioblastoma multiforme (GBM) is a highly malignant tumor. In spite of advances in surgery, chemotherapy, and radiotherapy, the life expectancy of the patient with glioblastoma is approximately 11 months. To enhance glioma-specific gene delivery, we employed a 12-mer phage display peptide library to isolate phages that bind specifically to human glioma cell lines. Here, we report the isolation and functional characterization of novel glioma-specific peptides that target transgenes specifically to a wide array of human glioblastomas in vitro and in vivo. One of the isolated peptides, tentatively denoted as MG11, is demonstrated to be glioma specific and gives an in vitro-binding enrichment of more than 5-fold for glioma cells when compared with nonglioma cells. Intravenous injection of phages bearing the MG11 peptide-binding motif enables the phages to home specifically to glioma xenografts. Most significantly, when Lissamine rhodamine-labeled MG11 peptide is injected intratumorally, it targets specifically to glioma xenografts instead of non-glioma-derived xenografts. In summary, our results suggest that the MG11 peptide is able to target specifically to tumors of glial origin, which would allow the design of applications related to the diagnosis and treatment of human gliomas.
Collapse
Affiliation(s)
- Ivy A W Ho
- Division of Cellular and Molecular Research, Gene Vector Laboratory, National Cancer Centre, Singapore 169610
| | | | | |
Collapse
|
42
|
Jiang B, Liu W, Qu H, Meng L, Song S, Ouyang T, Shou C. A Novel Peptide Isolated from a Phage Display Peptide Library with Trastuzumab Can Mimic Antigen Epitope of HER-2. J Biol Chem 2005; 280:4656-62. [PMID: 15536075 DOI: 10.1074/jbc.m411047200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Trastuzumab, a humanized antibody to HER-2, has been shown to be effective in the treatment of breast cancer in which HER-2 overexpression and metastasis occurs. In our search for an effective mimic epitope of HER-2 binding with trastuzumab and to develop HER-2 peptide vaccine, we screened a phage display 12-mer peptide library with trastuzumab as the target. A mimetic peptide (mimotope) H98 (LLGPYELWELSH) that could specifically recognize trastuzumab was isolated. The DNA encoding peptide H98 was cloned and expressed as the fusion protein GST-H98 in Escherichia coli BL21. The purified GST-H98 could specifically bind to trastuzumab and block the binding of trastuzumab to HER-2 protein. Moreover, H98 could significantly block the function of trastuzumab inhibiting the growth of cancer cells. Mice that were immunized with GST-H98 made specific antibody to H98 as well as to HER-2. In addition, T-cell proliferation occurred in mice immunized with GST-H98. Although no sequence homology was found between H98 and HER-2, through the use of structure analysis we were able to determine that peptide H98 contributed to a conformational epitope of HER-2. Furthermore, we determined that the last two amino acids at the C terminus, and the third together with the fourth amino acid at the N terminus of peptide H98 are critical to the binding of H98 to trastuzumab. As a result, we conclude that peptide H98 has potential for being developed as a HER-2 vaccine for biotherapy of cancer with HER-2 overexpression.
Collapse
MESH Headings
- Animals
- Antibodies, Monoclonal/pharmacology
- Antibodies, Monoclonal, Humanized
- Antigens/chemistry
- Antineoplastic Agents/pharmacology
- Binding, Competitive
- Blotting, Western
- Cell Line, Tumor
- Coloring Agents/pharmacology
- DNA/metabolism
- Dose-Response Relationship, Drug
- Enzyme-Linked Immunosorbent Assay
- Epitopes/chemistry
- Escherichia coli/metabolism
- Genetic Vectors
- Glutathione Transferase/metabolism
- Humans
- Immunoglobulin G/chemistry
- Mice
- Mice, Inbred BALB C
- Models, Molecular
- Mutation
- NIH 3T3 Cells
- Neoplasms/therapy
- Peptide Library
- Peptides/chemistry
- Protein Binding
- Protein Conformation
- Protein Structure, Tertiary
- Receptor, ErbB-2/chemistry
- Recombinant Fusion Proteins/metabolism
- Recombinant Proteins/chemistry
- Spleen/metabolism
- T-Lymphocytes/metabolism
- Tetrazolium Salts/pharmacology
- Thiazoles/pharmacology
- Trastuzumab
Collapse
Affiliation(s)
- Beihai Jiang
- Department of Biochemistry and Molecular Biology, Beijing Institute for Cancer Research and Peking University School of Oncology, Beijing 100034, China
| | | | | | | | | | | | | |
Collapse
|
43
|
Saxinger C, Conrads TP, Goldstein DJ, Veenstra TD. Fully automated synthesis of (phospho)peptide arrays in microtiter plate wells provides efficient access to protein tyrosine kinase characterization. BMC Immunol 2005; 6:1. [PMID: 15647109 PMCID: PMC546003 DOI: 10.1186/1471-2172-6-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Accepted: 01/12/2005] [Indexed: 01/15/2023] Open
Abstract
Background Synthetic peptides have played a useful role in studies of protein kinase substrates and interaction domains. Synthetic peptide arrays and libraries, in particular, have accelerated the process. Several factors have hindered or limited the applicability of various techniques, such as the need for deconvolution of combinatorial libraries, the inability or impracticality of achieving full automation using two-dimensional or pin solid phases, the lack of convenient interfacing with standard analytical platforms, or the difficulty of compartmentalization of a planar surface when contact between assay components needs to be avoided. This paper describes a process for synthesis of peptides and phosphopeptides on microtiter plate wells that overcomes previous limitations and demonstrates utility in determination of the epitope of an autophosphorylation site phospho-motif antibody and utility in substrate utilization assays of the protein tyrosine kinase, p60c-src. Results The overall reproducibility of phospho-peptide synthesis and multiplexed EGF receptor (EGFR) autophosphorylation site (pY1173) antibody ELISA (9H2) was within 5.5 to 8.0%. Mass spectrometric analyses of the released (phospho)peptides showed homogeneous peaks of the expected molecular weights. An overlapping peptide array of the complete EGFR cytoplasmic sequence revealed a high redundancy of 9H2 reactive sites. The eight reactive phospopeptides were structurally related and interestingly, the most conserved antibody reactive peptide motif coincided with a subset of other known EGFR autophosphorylation and SH2 binding motifs and an EGFR optimal substrate motif. Finally, peptides based on known substrate specificities of c-src and related enzymes were synthesized in microtiter plate array format and were phosphorylated by c-Src with the predicted specificities. The level of phosphorylation was proportional to c-Src concentration with sensitivities below 0.1 Units of enzyme. Conclusions The ability of this method to interface with various robotics and instrumentation is highly flexible since the microtiter plate is an industry standard. It is highly scalable by increasing the surface area within the well or the number of wells and does not require specialized robotics. The microtiter plate array system is well suited to the study of protein kinase substrates, antigens, binding molecules, and inhibitors since these all can be quantitatively studied at a single uniform, reproducible interface.
Collapse
Affiliation(s)
- Carl Saxinger
- Center for Cancer Research, NCI, Building 1052, Frederick, MD, 21702, USA
| | - Thomas P Conrads
- Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick Inc., National Cancer Institute at Frederick, PO Box B, Frederick, MD, 21702, USA
| | - David J Goldstein
- Center for Cancer Research, NCI, Building 31, Bethesda, MD 20892, USA
| | - Timothy D Veenstra
- Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick Inc., National Cancer Institute at Frederick, PO Box B, Frederick, MD, 21702, USA
| |
Collapse
|
44
|
Luo W, Hsu JCF, Kieber-Emmons T, Wang X, Ferrone S. Human tumor associated antigen mimicry by xenoantigens, anti-idiotypic antibodies and peptide mimics: Implications for immunotherapy of malignant diseases. ACTA ACUST UNITED AC 2005; 22:769-87. [PMID: 16110640 DOI: 10.1016/s0921-4410(04)22036-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- Wei Luo
- Department of Immunology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | | | | | | | | |
Collapse
|
45
|
Abstract
With an information explosion on the molecular mechanism of oncogenesis, the completion of the human genome sequence project, and the advances in genomic and proteomic methods, many therapeutic targets for various cancers have been identified. It is timely that a number of new drug development techniques have been developed in this last decade. Candidate drug targets can now be efficiently validated with RNA interference and transgenic animals studies. Combinatorial chemistry provides large numbers of chemical compounds for drug lead discovery and optimization. High throughput assays and high content cell-based assays, in conjunction with sophisticated robotics, are now available for screening large numbers of compounds. Based on X-ray crystallographic structure data, drug leads can be discovered through in silico screening of virtual libraries. By applying these various drug discovery techniques, it is anticipated that more potent and specific anti-cancer agents will be discovered within the next decade.
Collapse
Affiliation(s)
- Ruiwu Liu
- Division of Hematology & Oncology, Department of Internal Medicine, UC Davis Cancer Center, University of California at Davis, 4501 X Street, Sacramento, CA 95817, USA
| | | | | |
Collapse
|
46
|
Sweier DG, Shelburne CE, Cameron J, Lopatin DE. Localizing antibody-defined immunoreactivity in Porphyromonas gingivalis HtpG recognized by human serum utilizing selective protein expression. J Immunol Methods 2004; 285:165-70. [PMID: 14980431 DOI: 10.1016/j.jim.2003.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2003] [Revised: 11/19/2003] [Accepted: 11/24/2003] [Indexed: 11/24/2022]
Abstract
Earlier studies suggested that specific immunoreactive domains of the prokaryotic homologue of Hsp90, HtpG, might contribute to the virulence of the periodontal pathogen, Porphyromonas gingivalis (Pg) [J. Periodontol. 70 (1999) 1185]. Since serum antibodies to this protein appeared to be associated with oral health, we developed a rapid epitope-mapping system that could be tailored to detect antibodies against specific immunoreactive regions of the Pg HtpG protein. This paper describes the use of Caulobacter crescentus (Cc) and the creation of a Cc RsaA fusion protein library that defined specific regions of the Pg HtpG protein. The fusion protein library was used to identify immunoreactive regions in the Pg HtpG dominant in patient and control sera. The development of methods to rapidly localize dominant immunoreactive regions in protein antigens may prove useful for the development of screening tests, vaccines and therapeutics in periodontal and other infectious diseases.
Collapse
Affiliation(s)
- Domenica G Sweier
- Department of Biologic and Materials Sciences, School of Dentistry, The University of Michigan, 1011 North University Avenue, Campus Box 1078, Ann Arbor, MI 48109-1078, USA.
| | | | | | | |
Collapse
|
47
|
Crawford F, Huseby E, White J, Marrack P, Kappler JW. Mimotopes for alloreactive and conventional T cells in a peptide-MHC display library. PLoS Biol 2004; 2:E90. [PMID: 15094798 PMCID: PMC387264 DOI: 10.1371/journal.pbio.0020090] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2003] [Accepted: 01/21/2004] [Indexed: 12/29/2022] Open
Abstract
The use of peptide libraries for the identification and characterization of T cell antigen peptide epitopes and mimotopes has been hampered by the need to form complexes between the peptides and an appropriate MHC molecule in order to construct a complete T cell ligand. We have developed a baculovirus-based peptide library method in which the sequence encoding the peptide is embedded within the genes for the MHC molecule in the viral DNA, such that insect cells infected with virus encoding a library of different peptides each displays a unique peptide-MHC complex on its surface. We have fished in such a library with two different fluorescent soluble T cell receptors (TCRs), one highly peptide specific and the other broadly allo-MHC specific and hypothesized to be much less focused on the peptide portion of the ligand. A single peptide sequence was selected by the former alphabetaTCR that, not unexpectedly, was highly related to the immunizing peptide. As hypothesized, the other alphabetaTCR selected a large family of peptides, related only by a similarity to the immunizing peptide at the p5 position. These findings have implications for the relative importance of peptide and MHC in TCR ligand recognition. This display method has broad applications in T cell epitope identification and manipulation and should be useful in general in studying interactions between complex proteins.
Collapse
Affiliation(s)
- Frances Crawford
- 1Howard Hughes Medical Institute, Integrated Department of ImmunologyNational Jewish Medical and Research Center, Denver, ColoradoUnited States of America
- 2Integrated Department of Immunology, University of Colorado Health Science CenterDenver, ColoradoUnited States of America
| | - Eric Huseby
- 1Howard Hughes Medical Institute, Integrated Department of ImmunologyNational Jewish Medical and Research Center, Denver, ColoradoUnited States of America
- 2Integrated Department of Immunology, University of Colorado Health Science CenterDenver, ColoradoUnited States of America
| | - Janice White
- 1Howard Hughes Medical Institute, Integrated Department of ImmunologyNational Jewish Medical and Research Center, Denver, ColoradoUnited States of America
| | - Philippa Marrack
- 1Howard Hughes Medical Institute, Integrated Department of ImmunologyNational Jewish Medical and Research Center, Denver, ColoradoUnited States of America
- 2Integrated Department of Immunology, University of Colorado Health Science CenterDenver, ColoradoUnited States of America
- 3Department of Biochemistry and Molecular Genetics, University of Colorado Health Science CenterDenver, ColoradoUnited States of America
| | - John W Kappler
- 1Howard Hughes Medical Institute, Integrated Department of ImmunologyNational Jewish Medical and Research Center, Denver, ColoradoUnited States of America
- 2Integrated Department of Immunology, University of Colorado Health Science CenterDenver, ColoradoUnited States of America
- 4Department of Pharmacology and the Program in Biomolecular Structure, University of Colorado Health Science CenterDenver, ColoradoUnited States of America
| |
Collapse
|
48
|
|
49
|
Smith AH, Vrtis JM, Kodadek T. The Potential Of Protein-Detecting MicroArrays For Clinical Diagnostics. Adv Clin Chem 2004; 38:217-38. [PMID: 15521193 DOI: 10.1016/s0065-2423(04)38007-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Alexandra H Smith
- Department of Internal Medicine and Molecular Biology, Center for Biomedical Inventions, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | | | | |
Collapse
|