1
|
Hutchings CJ, Sato AK. Phage display technology and its impact in the discovery of novel protein-based drugs. Expert Opin Drug Discov 2024; 19:887-915. [PMID: 39074492 DOI: 10.1080/17460441.2024.2367023] [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] [Received: 11/28/2023] [Accepted: 06/07/2024] [Indexed: 07/31/2024]
Abstract
INTRODUCTION Phage display technology is a well-established versatile in vitro display technology that has been used for over 35 years to identify peptides and antibodies for use as reagents and therapeutics, as well as exploring the diversity of alternative scaffolds as another option to conventional therapeutic antibody discovery. Such successes have been responsible for spawning a range of biotechnology companies, as well as many complementary technologies devised to expedite the drug discovery process and resolve bottlenecks in the discovery workflow. AREAS COVERED In this perspective, the authors summarize the application of phage display for drug discovery and provide examples of protein-based drugs that have either been approved or are being developed in the clinic. The amenability of phage display to generate functional protein molecules to challenging targets and recent developments of strategies and techniques designed to harness the power of sampling diverse repertoires are highlighted. EXPERT OPINION Phage display is now routinely combined with cutting-edge technologies to deep-mine antibody-based repertoires, peptide, or alternative scaffold libraries generating a wealth of data that can be leveraged, e.g. via artificial intelligence, to enable the potential for clinical success in the discovery and development of protein-based therapeutics.
Collapse
|
2
|
Talotta R, Atzeni F, Laska MJ. Therapeutic peptides for the treatment of systemic lupus erythematosus: a place in therapy. Expert Opin Investig Drugs 2020; 29:845-867. [PMID: 32500750 DOI: 10.1080/13543784.2020.1777983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Studies in vitro and in vivo have identified several peptides that are potentially useful in treating systemic lupus erythematosus (SLE). The rationale for their use lies in the cost-effective production, high potency, target selectivity, low toxicity, and a peculiar mechanism of action that is mainly based on the induction of immune tolerance. Three therapeutic peptides have entered clinical development, but they have yielded disappointing results. However, some subsets of patients, such as those with the positivity of anti-dsDNA antibodies, appear more likely to respond to these medications. AREAS COVERED This review evaluates the potential use of therapeutic peptides for SLE and gives an opinion on how they may offer advantages for SLE treatment. EXPERT OPINION Given their acceptable safety profile, therapeutic peptides could be added to agents traditionally used to treat SLE and this may offer a synergistic and drug-sparing effect, especially in selected patient populations. Moreover, they could temporarily be utilized to manage SLE flares, or be administered as a vaccine in subjects at risk. Efforts to ameliorate bioavailability, increase the half-life and prevent immunogenicity are ongoing. The formulation of hybrid compounds, like peptibodies or peptidomimetic small molecules, is expected to yield renewed treatments with a better pharmacologic profile and increased efficacy.
Collapse
Affiliation(s)
- Rossella Talotta
- Department of Clinical and Experimental Medicine, Rheumatology Unit, Azienda Ospedaliera "Gaetano Martino", University of Messina , Messina, Italy
| | - Fabiola Atzeni
- Department of Clinical and Experimental Medicine, Rheumatology Unit, Azienda Ospedaliera "Gaetano Martino", University of Messina , Messina, Italy
| | | |
Collapse
|
3
|
Humoral immune responses against gonadotropin releasing hormone elicited by immunization with phage-peptide constructs obtained via phage display. J Biotechnol 2015; 216:20-8. [PMID: 26456116 DOI: 10.1016/j.jbiotec.2015.10.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 07/30/2015] [Accepted: 10/05/2015] [Indexed: 12/16/2022]
Abstract
Phage display is based on genetic engineering of phage coat proteins resulting in fusion peptides displayed on the surface of phage particles. The technology is widely used for generation of phages with novel characteristics for numerous applications in biomedicine and far beyond. The focus of this study was on development of phage-peptide constructs that stimulate production of antibodies against gonadotropin releasing hormone (GnRH). Phage-peptide constructs that elicit production of neutralizing GnRH antibodies can be used for anti-fertility and anti-cancer applications. Phage-GnRH constructs were generated via selection from a phage display library using several types of GnRH antibodies as selection targets. Such phage constructs were characterized for sequence similarities to GnRH peptide and frequency of their occurrence in the selection rounds. Five of the constructs with suitable characteristics were tested in mice as a single dose 5×10(11) virions (vir) vaccine and were found to be able to stimulate production of GnRH-specific antibodies, but not to suppress testosterone (indirect indicator of GnRH antibody neutralizing properties). Next, one of the constructs was tested at a higher dose of 2×10(12) vir per mouse in combination with a poly(lactide-co-glycolide) (PLGA)-based adjuvant. This resulted in multifold increase in GnRH antibody production and significant reduction of serum testosterone, indicating that antibodies produced in response to the phage-GnRH immunization possess neutralizing properties. To achieve optimal immune responses for desired applications, phage-GnRH constructs can be modified with respect to flanking sequences of GnRH-like peptides displayed on phage. Anticipated therapeutic effects also might be attained using optimized phage doses, a combination of several constructs in a single treatment, or application of adjuvants and advanced phage delivery systems.
Collapse
|
4
|
Zhao Y, Hao X, Feng J, Shen B, Wei J, Sun J. The comparison of BLyS-binding peptides from phage display library and computer-aided design on BLyS–TACI interaction. Int Immunopharmacol 2015; 24:219-223. [DOI: 10.1016/j.intimp.2014.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 11/30/2014] [Accepted: 12/09/2014] [Indexed: 10/24/2022]
|
5
|
He ZY, He QH, Xu Y, Li YP, Liu X, Chen B, Lei D, Sun CH. Ochratoxin A Mimotope from Second-Generation Peptide Library and Its Application in Immunoassay. Anal Chem 2013; 85:10304-11. [DOI: 10.1021/ac402127t] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Zhen-yun He
- State Key Laboratory of Food Science and Technology,
Sino-Germany Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| | - Qing-hua He
- State Key Laboratory of Food Science and Technology,
Sino-Germany Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| | - Yang Xu
- State Key Laboratory of Food Science and Technology,
Sino-Germany Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| | - Yan-ping Li
- State Key Laboratory of Food Science and Technology,
Sino-Germany Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| | - Xing Liu
- State Key Laboratory of Food Science and Technology,
Sino-Germany Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| | - Bo Chen
- State Key Laboratory of Food Science and Technology,
Sino-Germany Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| | - Da Lei
- State Key Laboratory of Food Science and Technology,
Sino-Germany Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| | - Cheng-hao Sun
- State Key Laboratory of Food Science and Technology,
Sino-Germany Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| |
Collapse
|
6
|
Krumpe LR, Mori T. Potential of phage-displayed peptide library technology to identify functional targeting peptides. Expert Opin Drug Discov 2013; 2:525. [PMID: 20150977 DOI: 10.1517/17460441.2.4.525] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Combinatorial peptide library technology is a valuable resource for drug discovery and development. Several peptide drugs developed through phage-displayed peptide library technology are presently in clinical trials and the authors envision that phage-displayed peptide library technology will assist in the discovery and development of many more. This review attempts to compile and summarize recent literature on targeting peptides developed through peptide library technology, with special emphasis on novel peptides with targeting capacity evaluated in vivo.
Collapse
Affiliation(s)
- Lauren Rh Krumpe
- SAIC-Frederick, Inc., Molecular Targets Development Program, NCI-Frederick, Frederick, Maryland 21702, USA
| | | |
Collapse
|
7
|
Smith MW, Al-Jayyoussi G, Gumbleton M. Peptide sequences mediating tropism to intact blood-brain barrier: an in vivo biodistribution study using phage display. Peptides 2012; 38:172-80. [PMID: 22955033 DOI: 10.1016/j.peptides.2012.06.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 06/25/2012] [Accepted: 06/26/2012] [Indexed: 12/15/2022]
Abstract
Peptide motifs that demonstrate tropism for the blood brain barrier (BBB) are of real translational value in developing innovative delivery strategies for biological brain targeted therapies. In vivo peptide-phage display affords peptide selection against the full complement of biological markers within the correct cellular macro- and micro-environments. Here a stringent in vivo biopanning protocol was employed in the rat aimed at identifying cyclic 7-mer peptide motifs that mediate tropism to brain microvasculature. Five rounds of biopanning identified 349 unique peptide motifs in the brain tissue gray matter compartment (microvasculature and parenchyma). While in general no consensus was evident linking peptide physico-chemical properties and brain tropism, peptides bearing c-SxTSSTx-c or c-xxxSSTx-c motifs were found to be present in high abundance. Based on amino acid frequency distribution of the 349 unique peptides sequences a theoretical 'idealized' peptide pattern, c-PP(S/P)SSST-c, could be derived. For the most abundant experimental peptide sequence found in brain tissue, c-SYTSSTM-c, an in vivo pharmacokinetic and whole body tissue biodistribution study was performed. Based upon tissue exposure data (i.e. tissue AUC((0-infinity))) the sequence c-SYTSSTM-c efficiently retargeted phage virions to the brain providing an approximate 5-fold greater (P<0.05) accumulation in brain over control phage; in all other organs no significant (P>0.05) difference in tissue tropism between c-SYTSSTM-c and control phages were evident. This peptide and more generally the peptide motifs, -SxTSSTx- or -xxxSSTx-, warrant further investigation as agents mediating sequence-dependent tropism to brain microvasculature potentially able to deliver biologic cargo to the CNS.
Collapse
Affiliation(s)
- Mathew W Smith
- Cardiff School of Pharmacy & Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom
| | | | | |
Collapse
|
8
|
Abstract
Peptides are increasingly used as therapeutic and diagnostic agents. The combination of bacterial cell-surface display peptide libraries with magnetic- and fluorescence-activated cell sorting technologies provides an efficient and highly effective methodology to identify and engineer peptides for a growing number of molecular recognition applications. Here, detailed protocols for both the generation and screening of bacterial display peptide libraries are presented. The methods described enable the discovery and evolutionary optimization of protein-binding peptides, cell-specific peptides, and enzyme substrates for diverse biotechnology applications.
Collapse
Affiliation(s)
- Jennifer A Getz
- Department of Chemical Engineering, Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California, USA
| | | | | |
Collapse
|
9
|
Lindner T, Kolmar H, Haberkorn U, Mier W. DNA libraries for the construction of phage libraries: statistical and structural requirements and synthetic methods. Molecules 2011; 16:1625-41. [PMID: 21326140 PMCID: PMC6259622 DOI: 10.3390/molecules16021625] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 01/26/2011] [Accepted: 02/11/2011] [Indexed: 01/19/2023] Open
Abstract
Peptide-based molecular probes identified by bacteriophage (phage) display technology expand the peptide repertoire for in vivo diagnosis and therapy of cancer. Numerous peptides that bind cancer-associated antigens have been discovered by panning phage libraries. However, until now only few of the peptides selected by phage display have entered clinical applications. The success of phage derived peptides essentially depends on the quality of the library screened. This review summarizes the methods to achieve highly homogenous libraries that cover a maximal sequence space. Biochemical and chemical strategies for the synthesis of DNA libraries and the techniques for their integration into the viral genome are discussed in detail. A focus is set on the methods that enable the exclusion of disturbing sequences. In addition, the parameters that define the variability, the minimal numbers of copies per library and the use of alternating panning cycles to avoid the loss of selected hits are evaluated.
Collapse
Affiliation(s)
- Thomas Lindner
- Department of Nuclear Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 400, D-69120 Heidelberg, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Darmstadt University of Technology, Petersenstrase 22, 64287 Darmstadt, Germany
| | - Uwe Haberkorn
- Department of Nuclear Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 400, D-69120 Heidelberg, Germany
| | - Walter Mier
- Department of Nuclear Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 400, D-69120 Heidelberg, Germany
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +49-6221-56-7720; Fax: +49-6221-56-33629
| |
Collapse
|
10
|
Pande J, Szewczyk MM, Grover AK. Phage display: concept, innovations, applications and future. Biotechnol Adv 2010; 28:849-58. [PMID: 20659548 DOI: 10.1016/j.biotechadv.2010.07.004] [Citation(s) in RCA: 336] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2010] [Revised: 06/27/2010] [Accepted: 07/08/2010] [Indexed: 12/17/2022]
Abstract
Phage display is the technology that allows expression of exogenous (poly)peptides on the surface of phage particles. The concept is simple in principle: a library of phage particles expressing a wide diversity of peptides is used to select those that bind the desired target. The filamentous phage M13 is the most commonly used vector to create random peptide display libraries. Several methods including recombinant techniques have been developed to increase the diversity of the library. On the other extreme, libraries with various biases can be created for specific purposes. For instance, when the sequence of the peptide that binds the target is known, its affinity and selectivity can be increased by screening libraries created with limited mutagenesis of the peptide. Phage libraries are screened for binding to synthetic or native targets. The initial screening of library by basic biopanning has been extended to column chromatography including negative screening and competition between selected phage clones to identify high affinity ligands with greater target specificity. The rapid isolation of specific ligands by phage display is advantageous in many applications including selection of inhibitors for the active and allosteric sites of the enzymes, receptor agonists and antagonists, and G-protein binding modulatory peptides. Phage display has been used in epitope mapping and analysis of protein-protein interactions. The specific ligands isolated from phage libraries can be used in therapeutic target validation, drug design and vaccine development. Phage display can also be used in conjunction with other methods. The past innovations and those to come promise a bright future for this field.
Collapse
Affiliation(s)
- Jyoti Pande
- Department of Medicine, HSC 4N41 McMaster Univ, Hamilton, ON, Canada
| | | | | |
Collapse
|
11
|
Mapping of Taenia solium TSOL18 antigenic epitopes by phage display library. Parasitol Res 2010; 106:1151-7. [DOI: 10.1007/s00436-010-1786-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Accepted: 01/19/2010] [Indexed: 11/25/2022]
|
12
|
Kenrick SA, Daugherty PS. Bacterial display enables efficient and quantitative peptide affinity maturation. Protein Eng Des Sel 2010; 23:9-17. [PMID: 19903738 DOI: 10.1093/protein/gzp065] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A quantitative screening method was developed to enable isolation and affinity maturation of peptide ligands specific for a given target from peptide libraries displayed on the outer surface of Escherichia coli using multi-parameter flow cytometry. From a large, random 15-mer peptide library, screening identified a core motif of W-E/D-W-E/D that conferred binding to vascular endothelial growth factor (VEGF). One cycle of affinity maturation resulted in the identification of several families of VEGF-binding peptides having distinct consensus sequences, from which a preferred disulfide constraint emerged. In the second affinity maturation cycle, high affinity peptides were favored by the addition of a decoy protein that bound an adjacent epitope on the display scaffold. The decoy apparently reduced rebinding or avidity effects, and the resulting peptides exhibited consensus at 12 of 19 amino acid positions. Peptides identified and affinity matured using bacterial display were remarkably similar to the best affinity matured using phage display and exhibited comparable dissociation constants (within 2-fold; K(D) = 4.7 x 10(-7) M). Screening of bacterial-displayed peptide libraries using cytometry enabled optimization of screening conditions to favor affinity and specificity and rapid clonal characterization. Bacterial display thus provides a new quantitative tool for the discovery and evolutionary optimization of protein-specific peptide ligands.
Collapse
Affiliation(s)
- Sophia A Kenrick
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | | |
Collapse
|
13
|
Identification of binding peptides of the ADAM15 disintegrin domain using phage display. J Biosci 2009; 34:213-20. [DOI: 10.1007/s12038-009-0025-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
14
|
Abstract
Molecular imaging is at the forefront in the advancement of in-vivo diagnosis and monitoring of cancer. New peptide-based molecular probes to facilitate cancer detection are rapidly evolving. Peptide-based molecular probes that target apoptosis, angiogenesis, cell signaling and cell adhesion events are in place. Bacteriophage (phage) display technology, a molecular genetic approach to ligand discovery, is commonly employed to identify peptides as tumor-targeting molecules. The peptide itself may perhaps have functional properties that diminish tumor growth or metastasis. More often, a selected peptide is chemically synthesized, coupled to a radiotracer or fluorescent probe, and utilized in the development of new noninvasive molecular imaging probes. A myriad of peptides that bind cancer cells and cancer-associated antigens have been reported from phage library selections. Phage selections have also been performed in live animals to obtain peptides with optimal stability and targeting properties in vivo. To this point, few in-vitro, in-situ, or in-vivo selected peptides have shown success in the molecular imaging of cancer, the notable exception being vascular targeting peptides identified via in-vivo selections. The success of vasculature targeting peptides, such as those with an RGD motif that bind alpha(v)beta(3)integrin, may be due to the abundance and expression patterns of integrins in tumors and supporting vasculature. The discovery of molecular probes that bind tumor-specific antigens has lagged considerably. One promising means to expedite discovery is through the implementation of selected phage themselves as tumor-imaging agents in animals.
Collapse
Affiliation(s)
- Jessica Newton
- Department of Biochemistry, University of Missouri, M743 Medical Sciences Bldg., Columbia, MO 65212, USA
| | | |
Collapse
|
15
|
Bublil EM, Freund NT, Mayrose I, Penn O, Roitburd-Berman A, Rubinstein ND, Pupko T, Gershoni JM. Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm. Proteins 2007; 68:294-304. [PMID: 17427229 DOI: 10.1002/prot.21387] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mapping the epitope of an antibody is of great interest, since it contributes much to our understanding of the mechanisms of molecular recognition and provides the basis for rational vaccine design. Here we present Mapitope, a computer algorithm for epitope mapping. The algorithm input is a set of affinity isolated peptides obtained by screening phage display peptide-libraries with the antibody of interest. The output is usually 1-3 epitope candidates on the surface of the atomic structure of the antigen. We have systematically tested the performance of Mapitope by assessing the effect of the algorithm parameters on the final prediction. Thus, we have examined the effect of the statistical threshold (ST) parameter, relating to the frequency distribution and enrichment of amino acid pairs from the isolated peptides and the D (distance) and E (exposure) parameters which relate to the physical parameters of the antigen. Two model systems were analyzed in which the antibody of interest had previously been co-crystallized with the antigen and thus the epitope is a given. The Mapitope algorithm successfully predicted the epitopes in both models. Accordingly, we formulated a stepwise paradigm for the prediction of discontinuous conformational epitopes using peptides obtained from screening phage display libraries. We applied this paradigm to successfully predict the epitope of the Trastuzumab antibody on the surface of the Her-2/neu receptor in a third model system.
Collapse
Affiliation(s)
- Erez M Bublil
- Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, Israel
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Gershoni JM, Roitburd-Berman A, Siman-Tov DD, Tarnovitski Freund N, Weiss Y. Epitope mapping: the first step in developing epitope-based vaccines. BioDrugs 2007; 21:145-56. [PMID: 17516710 PMCID: PMC7100438 DOI: 10.2165/00063030-200721030-00002] [Citation(s) in RCA: 192] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Antibodies are an effective line of defense in preventing infectious diseases. Highly potent neutralizing antibodies can intercept a virus before it attaches to its target cell and, thus, inactivate it. This ability is based on the antibodies’ specific recognition of epitopes, the sites of the antigen to which antibodies bind. Thus, understanding the antibody/epitope interaction provides a basis for the rational design of preventive vaccines. It is assumed that immunization with the precise epitope, corresponding to an effective neutralizing antibody, would elicit the generation of similarly potent antibodies in the vaccinee. Such a vaccine would be a ‘B-cell epitope-based vaccine’, the implementation of which requires the ability to backtrack from a desired antibody to its corresponding epitope. In this article we discuss a range of methods that enable epitope discovery based on a specific antibody. Such a reversed immunological approach is the first step in the rational design of an epitope-based vaccine. Undoubtedly, the gold standard for epitope definition is x-ray analyses of crystals of antigen: antibody complexes. This method provides atomic resolution of the epitope; however, it is not readily applicable to many antigens and antibodies, and requires a very high degree of sophistication and expertise. Most other methods rely on the ability to monitor the binding of the antibody to antigen fragments or mutated variations. In mutagenesis of the antigen, loss of binding due to point modification of an amino acid residue is often considered an indication of an epitope component. In addition, computational combinatorial methods for epitope mapping are also useful. These methods rely on the ability of the antibody of interest to affinity isolate specific short peptides from combinatorial phage display peptide libraries. The peptides are then regarded as leads for the definition of the epitope corresponding to the antibody used to screen the peptide library. For epitope mapping, computational algorithms have been developed, such as Mapitope, which has recently been found to be effective in mapping conformational discontinuous epitopes. The pros and cons of various approaches towards epitope mapping are also discussed.
Collapse
Affiliation(s)
- Jonathan M Gershoni
- Department of Cell Research and Immunology, Tel Aviv University, Tel-Aviv, Israel.
| | | | | | | | | |
Collapse
|
17
|
Liu FF, Wang T, Dong XY, Sun Y. Rational design of affinity peptide ligand by flexible docking simulation. J Chromatogr A 2007; 1146:41-50. [PMID: 17298835 DOI: 10.1016/j.chroma.2007.01.130] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2006] [Revised: 01/05/2007] [Accepted: 01/25/2007] [Indexed: 10/23/2022]
Abstract
Rational design of affinity peptide ligands of proteins by flexible docking simulation is performed using the SYBYL program package. This approach involves the use of experimental data to verify a scoring function that can be used to assess the affinity of a peptide for its target protein. The enzyme-linked immunosorbent assay (ELISA) data of several peptides displayed on phage surfaces for insulin and lysozyme, respectively, reported in literature are used for the purpose. It is found that the absolute values of the Dscore calculated from the docking correspond well to the ELISA data that relate to the affinity between the peptides and the target molecule. So, the Dscore function is used to assess the affinity of docked peptides in a pentapeptide library designed on the basis of protein (alpha-amylase) structure. As a result, a pentapeptide with a high Dscore value is selected and a hexapeptide (FHENWS) is built by linking serine to its C-terminal to lengthen the peptide. Molecular surface analysis with the MOLCAD program reveals that electrostatic interactions (including hydrogen bonds) and Van der Waals forces contribute to the affinity of the hexapeptide for alpha-amylase. Chromatographic experiments with the immobilized peptide have given further evidence for this observation. Adsorption isotherm described by the Langmuir equation indicates that the apparent binding constant of alpha-amylase to the immobilized hexapeptide was 2.5x10(5)L/mol. Finally, high affinity and specificity of the affinity adsorbent is exemplified by the purification of alpha-amylase from crude fermentation broth of Bacillus subtilis.
Collapse
Affiliation(s)
- Fu-Feng Liu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | | | | | | |
Collapse
|
18
|
Sato AK, Viswanathan M, Kent RB, Wood CR. Therapeutic peptides: technological advances driving peptides into development. Curr Opin Biotechnol 2006; 17:638-42. [PMID: 17049837 DOI: 10.1016/j.copbio.2006.10.002] [Citation(s) in RCA: 253] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2006] [Revised: 08/23/2006] [Accepted: 10/06/2006] [Indexed: 12/31/2022]
Abstract
As potential therapeutics, peptides offer several advantages over small molecules (increased specificity) and antibodies (small size). Nevertheless, a number of key issues have hampered their use as drug candidates. A series of new technologies have recently been developed that allow peptides to be viable drug candidates in areas usually restricted to protein therapeutics, such as monoclonal antibodies. These include the development of various types of peptide-conjugates that have lower rates of clearance and hence the potential to increase the exposure of peptide drug candidates in chronic diseases. Structural additions have also been made to peptides, including the use of unnatural amino acids, mainchain modifications and other novel substitutions, which have helped to improve peptide stability and further their therapeutic potential.
Collapse
Affiliation(s)
- Aaron K Sato
- Dyax Corporation, 300 Technology Square, Cambridge, MA 02139, USA
| | | | | | | |
Collapse
|
19
|
Piszczek G. Luminescent metal-ligand complexes as probes of macromolecular interactions and biopolymer dynamics. Arch Biochem Biophys 2006; 453:54-62. [PMID: 16603119 DOI: 10.1016/j.abb.2006.03.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2006] [Accepted: 03/05/2006] [Indexed: 11/26/2022]
Abstract
The knowledge of microsecond dynamics is important for an understanding of the mechanism and function of biological systems. Fluorescent techniques are well established in biophysical studies, but their applicability to probe microsecond timescale processes is limited. Luminescent metal-ligand complexes (MLCs) have created interest mainly due to their unique luminescent properties, such as the exceptionally long decay times and large fundamental anisotropy values, allowing examination of microsecond dynamics by fluorescence methods. MLC properties also greatly simplify instrumentation requirements and enable the use of light emitting diode excitation for time-resolved measurements. Recent literature illustrates how MLC labels take full advantage of well developed fluorescence techniques and how those methods can be extended to timescales not easily accessible with nanosecond probes. MLCs are now commercially available as reactive labels which give researchers access to methods that previously required more complex approaches. The present paper gives an overview of the applications of MLC probes to studies of molecular dynamics and interactions of proteins, membranes and nucleic acids.
Collapse
Affiliation(s)
- Grzegorz Piszczek
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
20
|
Haiat S, Billard C, Quiney C, Ajchenbaum-Cymbalista F, Kolb JP. Role of BAFF and APRIL in human B-cell chronic lymphocytic leukaemia. Immunology 2006; 118:281-92. [PMID: 16827889 PMCID: PMC1782305 DOI: 10.1111/j.1365-2567.2006.02377.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
B-cell chronic lymphocytic leukaemia (B-CLL) is the most prevalent leukaemia in Western countries and is characterized by the gradual accumulation in patients of small mature B cells. Since the vast majority of tumoral cells are quiescent, the accumulation mostly results from deficient apoptosis rather than from acute proliferation. Although the phenomenon is relevant in vivo, B-CLL cells die rapidly in vitro as a consequence of apoptosis, suggesting a lack of essential growth factors in the culture medium. Indeed, the rate of B-CLL cell death in vitro is modulated by different cytokines, some favouring the apoptotic process, others counteracting it. Two related members of the tumour necrosis factor family, BAFF (B-cell activating factor of the TNF family) and APRIL (a proliferation-inducing ligand), already known for their crucial role in normal B-cell survival, differentiation and apoptosis, were recently shown to be expressed by B-CLL cells. These molecules are able to protect the leukaemic cells against spontaneous and drug-induced apoptosis via autocrine and/or paracrine pathways. This review will focus on the role of BAFF and APRIL in the survival of tumoral cells. It will discuss the expression of these molecules by B-CLL cells, their regulation, transduction pathways and their effects on leukaemic cells. The design of reagents able to counteract the effects of these molecules seems to be a new promising therapeutic approach for B-CLL and is already currently developed in the treatment of autoimmune diseases.
Collapse
Affiliation(s)
- Stéphanie Haiat
- UMRS INSERM 736/University Paris 6, Centre de Recherches Biomédicales des CordeliersParis
| | - Christian Billard
- UMRS INSERM 736/University Paris 6, Centre de Recherches Biomédicales des CordeliersParis
| | - Claire Quiney
- UMRS INSERM 736/University Paris 6, Centre de Recherches Biomédicales des CordeliersParis
| | | | - Jean-Pierre Kolb
- UMRS INSERM 736/University Paris 6, Centre de Recherches Biomédicales des CordeliersParis
| |
Collapse
|
21
|
Fletcher KA, Fakayode SO, Lowry M, Tucker SA, Neal SL, Kimaru IW, McCarroll ME, Patonay G, Oldham PB, Rusin O, Strongin RM, Warner IM. Molecular fluorescence, phosphorescence, and chemiluminescence spectrometry. Anal Chem 2006; 78:4047-68. [PMID: 16771540 PMCID: PMC2662353 DOI: 10.1021/ac060683m] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
22
|
Krumpe LR, Mori T. The Use of Phage-Displayed Peptide Libraries to Develop Tumor-Targeting Drugs. Int J Pept Res Ther 2006; 12:79-91. [PMID: 19444323 PMCID: PMC2678933 DOI: 10.1007/s10989-005-9002-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2005] [Indexed: 01/13/2023]
Abstract
Monoclonal antibodies have been successfully utilized as cancer-targeting therapeutics and diagnostics, but the efficacies of these treatments are limited in part by the size of the molecules and non-specific uptake by the reticuloendothelial system. Peptides are much smaller molecules that can specifically target cancer cells and as such may alleviate complications with antibody therapy. Although many endogenous and exogenous peptides have been developed into clinical therapeutics, only a subset of these consists of cancer-targeting peptides. Combinatorial biological libraries such as bacteriophage-displayed peptide libraries are a resource of potential ligands for various cancer-related molecular targets. Target-binding peptides can be affinity selected from complex mixtures of billions of displayed peptides on phage and further enriched through the biopanning process. Various cancer-specific ligands have been isolated by in vitro, in vivo, and ex vivo screening methods. As several peptides derived from phage-displayed peptide library screenings have been developed into therapeutics in current clinical trials, which validates peptide-targeting potential, the use of phage display to identify cancer-targeting therapeutics should be further exploited.
Collapse
Affiliation(s)
- Lauren R.H. Krumpe
- Basic Research Program, Science Applications International Corporation-Frederick, Inc., Frederick, MD USA
| | - Toshiyuki Mori
- Molecular Targets Development Program, Center for Cancer Research, National Cancer Institute, Frederick, MD USA
- Biomedical Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 2-17-85 Yodogawaku, Osaka, 532-8686 Japan
| |
Collapse
|
23
|
Elsawa SF, Novak AJ, Grote DM, Ziesmer SC, Witzig TE, Kyle RA, Dillon SR, Harder B, Gross JA, Ansell SM. B-lymphocyte stimulator (BLyS) stimulates immunoglobulin production and malignant B-cell growth in Waldenstrom macroglobulinemia. Blood 2005; 107:2882-8. [PMID: 16304043 PMCID: PMC1895377 DOI: 10.1182/blood-2005-09-3552] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Waldenström macroglobulinemia (WM) is a serious and frequently fatal B-cell malignancy associated with an elevated monoclonal IgM protein in the serum. Many of the mechanisms leading to this disease are not yet known. B-lymphocyte stimulator (BLyS) is a TNF family member that is critical for maintenance of normal B-cell development and homeostasis. BLyS is overexpressed in a variety of B-cell malignancies and has been shown to inhibit apoptosis in malignant B cells. It also regulates immunoglobulin secretion by normal B cells. To determine the relevance of BLyS in WM, we examined the role of BLyS in WM patient samples. Malignant B cells were found to bind soluble BLyS and variably express the receptors BAFF-R, TACI, and BCMA. We also found expression of BLyS in bone marrow specimens by immunohistochemistry and elevated serum BLyS levels in patients with WM. BLyS, alone or in combination with cytokines that induce immunoglobulin production, was found to increase IgM secretion by malignant B cells. Furthermore, BLyS was found to increase the viability and proliferation of malignant B cells from WM patients. Due to the role of BLyS in WM, strategies to inhibit BLyS may potentially have therapeutic efficacy in these patients.
Collapse
Affiliation(s)
- Sherine F Elsawa
- Division of Hematology and Internal Medicine, Mayo Clinic, 200 First St SW, Rochester, MN 55905.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Levin AM, Weiss GA. Optimizing the affinity and specificity of proteins with molecular display. MOLECULAR BIOSYSTEMS 2005; 2:49-57. [PMID: 16880922 DOI: 10.1039/b511782h] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Affinity maturation of receptor-ligand interactions represents an important area of academic and pharmaceutical research. Improving affinity and specificity of proteins can tailor potency for both in vivo and in vitro applications. A number of different display platforms including phage display, bacterial and yeast display, ribosome display, and mRNA display can optimize protein affinity and specificity. Here, we will review the advantages and disadvantages of these molecular display methods with a focus on their suitability for protein affinity maturation.
Collapse
Affiliation(s)
- A M Levin
- Department of Chemistry, University of California, Irvine, CA 92697, USA
| | | |
Collapse
|
25
|
Shrivastava A, von Wronski MA, Sato AK, Dransfield DT, Sexton D, Bogdan N, Pillai R, Nanjappan P, Song B, Marinelli E, DeOliveira D, Luneau C, Devlin M, Muruganandam A, Abujoub A, Connelly G, Wu QL, Conley G, Chang Q, Tweedle MF, Ladner RC, Swenson RE, Nunn AD. A distinct strategy to generate high-affinity peptide binders to receptor tyrosine kinases. Protein Eng Des Sel 2005; 18:417-24. [PMID: 16087652 DOI: 10.1093/protein/gzi049] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We describe a novel and general way of generating high affinity peptide (HAP) binders to receptor tyrosine kinases (RTKs), using a multi-step process comprising phage-display selection, identification of peptide pairs suitable for hetero-dimerization (non-competitive and synergistic) and chemical synthesis of heterodimers. Using this strategy, we generated HAPs with K(D)s below 1 nM for VEGF receptor-2 (VEGFR-2) and c-Met. VEGFR-2 HAPs bound significantly better (6- to 500-fold) than either of the individual peptides that were used for heterodimer synthesis. Most significantly, HAPs were much better (150- to 800-fold) competitors than monomers of the natural ligand (VEGF) in various competitive binding and functional assays. In addition, we also found the binding of HAPs to be less sensitive to serum than their component peptides. We believe that this method may be applied to any protein for generating high affinity peptide (HAP) binders.
Collapse
Affiliation(s)
- A Shrivastava
- Ernst Felder Laboratories, Bracco Research USA, Princeton, NJ 08540, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Ladner RC, Sato AK, Gorzelany J, de Souza M. Phage display-derived peptides as therapeutic alternatives to antibodies. Drug Discov Today 2004; 9:525-9. [PMID: 15183160 DOI: 10.1016/s1359-6446(04)03104-6] [Citation(s) in RCA: 201] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Peptide-based drugs are now viable alternatives to biopharmaceuticals, such as antibodies. Most of the past limitations of peptides have been removed by new technologies, so that peptides now face similar hurdles to antibodies. Phage-display technology provides novel peptides that bind protein targets with high affinity and specificity. Most marketed peptide-based drugs are receptor agonists derived from natural peptides. To address the need for antagonists, novel strategies have been developed for inhibiting receptor-ligand interactions. We review results from phage display in finding peptide drug candidates and conclude with some business benefits of developing peptides.
Collapse
|