1
|
Kume A, Kawai S, Kato R, Iwata S, Shimizu K, Honda H. Exploring high-affinity binding properties of octamer peptides by principal component analysis of tetramer peptides. J Biosci Bioeng 2016; 123:230-238. [PMID: 27618533 DOI: 10.1016/j.jbiosc.2016.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 07/25/2016] [Accepted: 08/17/2016] [Indexed: 11/24/2022]
Abstract
To investigate the binding properties of a peptide sequence, we conducted principal component analysis (PCA) of the physicochemical features of a tetramer peptide library comprised of 512 peptides, and the variables were reduced to two principal components. We selected IL-2 and IgG as model proteins and the binding affinity to these proteins was assayed using the 512 peptides mentioned above. PCA of binding affinity data showed that 16 and 18 variables were suitable for localizing IL-2 and IgG high-affinity binding peptides, respectively, into a restricted region of the PCA plot. We then investigated whether the binding affinity of octamer peptide libraries could be predicted using the identified region in the tetramer PCA. The results show that octamer high-affinity binding peptides were also concentrated in the tetramer high-affinity binding region of both IL-2 and IgG. The average fluorescence intensity of high-affinity binding peptides was 3.3- and 2.1-fold higher than that of low-affinity binding peptides for IL-2 and IgG, respectively. We conclude that PCA may be used to identify octamer peptides with high- or low-affinity binding properties from data from a tetramer peptide library.
Collapse
Affiliation(s)
- Akiko Kume
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Shun Kawai
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Ryuji Kato
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Shinmei Iwata
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Kazunori Shimizu
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiroyuki Honda
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
| |
Collapse
|
2
|
Kruspe S, Mittelberger F, Szameit K, Hahn U. Aptamers as drug delivery vehicles. ChemMedChem 2014; 9:1998-2011. [PMID: 25130604 DOI: 10.1002/cmdc.201402163] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/02/2014] [Indexed: 01/22/2023]
Abstract
The benefits of directed and selective therapy for systemic treatment are reasons for increased interest in exploiting aptamers for cell-specific drug delivery. Nucleic acid based pharmaceuticals represent an interesting and novel tool to counter human diseases. Combining inhibitory potential and cargo transfer upon internalization, nanocarriers as well as various therapeutics including siRNAs, chemotherapeutics, photosensitizers, or proteins can be imported via these synthetic nucleic acids. However, widespread clinical application is still hampered by obstacles that must be overcome. In this review, we give an overview of applications and recent advances in aptamer-mediated drug delivery. We also introduce prominent selection methods as well as useful approaches in choice of drug and conjugation method. We discuss the challenges that need to be considered and present strategies that have been applied to achieve intracellular delivery of effectors transported by readily internalized aptamers.
Collapse
Affiliation(s)
- Sven Kruspe
- Institut für Biochemie und Molekularbiologie, Universität Hamburg, Martin-Luther-King Platz 6, 20146 Hamburg (Germany)
| | | | | | | |
Collapse
|
3
|
Hu Y, Duan J, Zhan Q, Wang F, Lu X, Yang XD. Novel MUC1 aptamer selectively delivers cytotoxic agent to cancer cells in vitro. PLoS One 2012; 7:e31970. [PMID: 22384115 PMCID: PMC3284512 DOI: 10.1371/journal.pone.0031970] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 01/19/2012] [Indexed: 11/18/2022] Open
Abstract
Chemotherapy is a primary treatment for cancer, but its efficacy is often limited by the adverse effects of cytotoxic agents. Targeted drug delivery may reduce the non-specific toxicity of chemotherapy by selectively directing anticancer drugs to tumor cells. MUC1 protein is an attractive target for tumor-specific drug delivery owning to its overexpression in most adenocarcinomas. In this study, a novel MUC1 aptamer is exploited as the targeting ligand for carrying doxorubicin (Dox) to cancer cells. We developed an 86-base DNA aptamer (MA3) that bound to a peptide epitope of MUC1 with a Kd of 38.3 nM and minimal cross reactivity to albumin. Using A549 lung cancer and MCF-7 breast cancer cells as MUC1-expressing models, MA3 was found to preferentially bind to MUC1-positive but not MUC1-negative cells. An aptamer-doxorubicin complex (Apt-Dox) was formulated by intercalating doxorubicin into the DNA structure of MA3. Apt-Dox was found capable of carrying doxorubicin into MUC1-positive tumor cells, while significantly reducing the drug intake by MUC1-negative cells. Moreover, Apt-Dox retained the efficacy of doxorubicin against MUC1-positive tumor cells, but lowered the toxicity to MUC1-negative cells (P<0.01). The results suggest that the MUC1 aptamer may have potential utility as a targeting ligand for selective delivery of cytotoxic agent to MUC1-expressing tumors.
Collapse
Affiliation(s)
- Yan Hu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jinhong Duan
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qimin Zhan
- Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fengdan Wang
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Lu
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xian-Da Yang
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- * E-mail:
| |
Collapse
|
4
|
Ferreira CSM, Papamichael K, Guilbault G, Schwarzacher T, Gariepy J, Missailidis S. DNA aptamers against the MUC1 tumour marker: design of aptamer-antibody sandwich ELISA for the early diagnosis of epithelial tumours. Anal Bioanal Chem 2007; 390:1039-50. [PMID: 17694298 DOI: 10.1007/s00216-007-1470-1] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2007] [Revised: 06/19/2007] [Accepted: 06/25/2007] [Indexed: 10/23/2022]
Abstract
Aptamers are functional molecules able to bind tightly and selectively to disease markers, offering great potential for applications in disease diagnosis and therapy. MUC1 is a well-known tumour marker present in epithelial malignancies and is used in immunotherapeutic and diagnostic approaches. We report the selection of DNA aptamers that bind with high affinity and selectivity an MUC1 recombinant protein containing five repeats of the variable tandem repeat region. Aptamers were selected using the SELEX methodology from an initial library containing a 25-base-long variable region for their ability to bind to the unglycosylated form of the MUC1 protein. After ten rounds of in vitro selection and amplification, more than 90% of the pool of sequences consisted of target-binding molecules, which were cloned, sequenced and found to share no sequence consensus. The binding properties of these aptamers were quantified using ELISA and surface plasmon resonance. The lead aptamer sequence was subsequently used in the design of an aptamer-antibody hybrid sandwich ELISA for the identification and quantification of MUC1 in buffered solutions. Following optimisation of the operating conditions, the resulting enzyme immunoassay displayed an EC50 value of 25 microg/ml, a detection limit of 1 microg/ml and a linear range between 8 and 100 microg/ml for the MUC1 five tandem repeat analyte. In addition, recovery studies performed in buffer conditions resulted in averaged recoveries between 98.2 and 101.7% for all spiked samples, demonstrating the usability of the aptamer as a receptor in microtitre-based assays. Our results aim towards the formation of new diagnostic assays against this tumour marker for the early diagnosis of primary or metastatic disease in breast, bladder and other epithelial tumours.
Collapse
Affiliation(s)
- C S M Ferreira
- Chemistry Department, The Open University, Walton Hall, Milton Keynes, MK7 6AA, UK
| | | | | | | | | | | |
Collapse
|
5
|
Mersich C, Billes W, Jungbauer A. Identification of a ligand for IgG-Fc derived from a soluble peptide library based on fusion proteins secreted byS. cerevisiae. Biotechnol J 2007; 2:672-7. [PMID: 17492714 DOI: 10.1002/biot.200700049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Biological libraries are important tools in the development of new peptide-based compounds. Here, we describe the use of a soluble peptide library system as a complementary tool in the field of ligand development. Random peptides were expressed in S. cerevisiae as carboxy-terminal extensions of the eukaryotic initiation factor 5a (eIF5a) and secreted into the culture supernatant. Expression and screening of this library were performed in a microwell format. As an example of this versatile approach, we describe the identification of a ligand for the human IgG-Fc fragment. Ligands binding IgG-Fc show great potential in a wide variety of applications including development of therapeutics, streamlining the large-scale purification of antibodies, and applications in diagnostic tests. We demonstrated the utility of this system. After screening only 6160 clones, we identified a ligand with the peptide sequence of TRRRTCSPPTWPRARARSTPSGCSSTGPSANRG. An affinity constant of 3.9 x 10(5) M(-1) was determined by a biosensor method. Handling and maintenance of this library is conceptually simple and highly applicable for automated high-throughput systems.
Collapse
Affiliation(s)
- Christa Mersich
- Department of Biotechnology, University of Natural Resources and Applied Life Sciences Vienna, Vienna, Austria
| | | | | |
Collapse
|
6
|
Ferreira CSM, Matthews CS, Missailidis S. DNA aptamers that bind to MUC1 tumour marker: design and characterization of MUC1-binding single-stranded DNA aptamers. Tumour Biol 2006; 27:289-301. [PMID: 17033199 DOI: 10.1159/000096085] [Citation(s) in RCA: 278] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2006] [Accepted: 02/15/2006] [Indexed: 01/01/2023] Open
Abstract
Agents able to bind tightly and selectively to disease markers can greatly benefit disease diagnosis and therapy. Aptamers are functional molecules, usually DNA or RNA oligonucleotides, with the appropriate sequence and structure to form a complex with a target molecule. MUC1 is a well-known tumour marker present in a variety of malignant tumours and it has been a target of interest for many years. In this work we report the selection of DNA aptamers that bind with high affinity and selectivity to the MUC1 peptides. Combinatorial chemistry techniques based on the SELEX methodology were used for the identification of the specific aptamers. These were selected from an initial library containing a 25-base-long variable region, resulting in 4(25) random sequences of single-stranded DNA molecules, for their ability to bind to synthetic forms of MUC1. Ten rounds of in vitro selection were performed enriching for MUC1 binding. By round ten more than 90% of the pool of sequences consisted of MUC1-binding molecules. Selected aptamer families were cloned, sequenced and found to be unique, sharing no sequence consensus. The binding properties of these aptamers were quantitated by enzyme-linked immunosorbent assay and surface plasmon resonance, whereas their specificity for MUC1-expressing cancer cells has been validated using fluorescent microscopy. Aptamers offer significant advantages over existing antibody-based recognition procedures in that they offer higher binding affinity (higher retention/reduced dissociation) and specificity to the target (ability to determine variations on the protein target down to single amino acid changes), higher selectivity against mutated protein epitopes and potentially reduced immunogenicity and increased tumour penetration associated with their size.
Collapse
Affiliation(s)
- C S M Ferreira
- Chemistry Department, The Open University, Milton Keynes, MK7 6AA, UK
| | | | | |
Collapse
|
7
|
Bellofiore P, Petronzelli F, De Martino T, Minenkova O, Bombardi V, Anastasi AM, Lindstedt R, Felici F, De Santis R, Verdoliva A. Identification and refinement of a peptide affinity ligand with unique specificity for a monoclonal anti-tenascin-C antibody by screening of a phage display library. J Chromatogr A 2006; 1107:182-91. [PMID: 16414054 DOI: 10.1016/j.chroma.2005.12.064] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2005] [Revised: 12/15/2005] [Accepted: 12/19/2005] [Indexed: 11/22/2022]
Abstract
Using phage display technology, a 22-mer peptide was selected as a ligand with unique specificity for the murine monoclonal ST2146 antibody that recognizes the EGF repeats region of the human tumor-associated antigen tenascin-C. This peptide, synthesized in an 8-branched form to enhance its binding properties, is useful in replacing the native antigen in the affinity and immunoreactivity characterization of the ST2146 antibody and its biotinylated derivatives. Affinity resins, prepared by immobilizing the mimotope or its shorter 10-mer binding unit on a chromatographic support, were able to capture ST2146 directly from the hybridoma supernatant, with antibody recovery and host cell protein (HCP) reduction similar to or better than protein A sorbent, a purity degree exceeding 95%, and full recovery of antibody activity. The affinity constants of both peptides, as determined by frontal analysis of broad-zone elution affinity chromatography and BiaCore measurements, were very similar and included in a range suitable for affinity ligands. Column capacity, determined by applying a large excess of purified ST2146 to 1 mL of column bed volume, was close to 50 mg/mL for both resins. These matrices retain their ST2146 binding properties after various treatments, including sanitization, thus indicating very high stability in terms of ligand leakage and degradation. Moreover, the short form shows higher enzymatic stability, thus proving more suitable as ligand for ST2146 affinity purification.
Collapse
Affiliation(s)
- Piero Bellofiore
- Tecnogen S.C.p.A., Località La Fagianeria, 81015 Piana di Monte Verna, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Roque ACA, Lowe CR. Advances and applications of de novo designed affinity ligands in proteomics. Biotechnol Adv 2006; 24:17-26. [PMID: 16006085 DOI: 10.1016/j.biotechadv.2005.05.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2005] [Accepted: 05/09/2005] [Indexed: 11/30/2022]
Abstract
Affinity chromatography represents a promising technique for decoding the proteomics universe. While conventional affinity purification is being used in conjunction with two-dimensional electrophoresis (2D-PAGE) and mass spectrometry (MS) for the study of proteomes and subproteomes, scientists are still confronted with the need for specific and tailor-made affinity ligands to target desired groups and families of proteins. Evidence has shown that, in many situations, synthetic affinity ligands can circumvent inconveniences associated with the utilisation of biological ligands for the chromatography-based purification of biomolecules. This review will highlight the potential applications of affinity chromatography and synthetic de novo designed ligands as separation tools for proteomics.
Collapse
|
9
|
Missailidis S, Thomaidou D, Borbas KE, Price MR. Selection of aptamers with high affinity and high specificity against C595, an anti-MUC1 IgG3 monoclonal antibody, for antibody targeting. J Immunol Methods 2005; 296:45-62. [PMID: 15680150 DOI: 10.1016/j.jim.2004.10.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2003] [Revised: 10/19/2004] [Accepted: 10/25/2004] [Indexed: 11/28/2022]
Abstract
Targeting of antibodies has found a number of applications in assays, anti-idiotypic therapies and vaccine design with a number of anti-idiotypic Abs generated and used in clinical applications, and some currently in clinical trials. Meanwhile, aptamers are a novel and particularly interesting targeting modality, with a unique ability to bind to a variety of targets. Aptamers offer unique benefits compared to other targeting agents, due to their high affinity and selectivity, relatively small size and in vitro synthesis, making them attractive alternatives to Abs and peptides. Aptamers have already been selected against a number of Abs for various applications. We now present a novel methodology for the selection of aptamers against Abs, which minimises the number of steps used and results in molecules that bind to the target Ab with high affinity and specificity. We have used the well-characterised anti-MUC1 monoclonal Ab C595 as an exemplar for raising aptamers against Abs. The methodology is based on the adsorption of the Ab to the surface of a PCR tube and the performance of SELEX selections in the PCR tube, based on elution steps resulting from the denaturation of the Ab on the first PCR amplification cycle. After 10 rounds of selection and amplification, selected aptamers have been characterised using a number of techniques, including fluorescence quenching, ELISA and competition ELISA procedures and a FRET type assay. Aptamers were found to bind their target Ab with a higher affinity than its natural antigenic peptide, as observed in fluorescent quenching and FRET experiments. Furthermore, they were able to displace the antigens from the antibody binding pocket in competition assays. This methodology offers the possibility of rapidly selecting aptamers for antibody targeting that could be used as diagnostic, imaging or therapeutic agents, or as recognition units in immunoassays, and can be potentially useful in raising aptamers against other protein targets.
Collapse
Affiliation(s)
- Sotiris Missailidis
- Chemistry Department, The Open University, Walton Hall, Milton Keynes MK7 6AA, UK.
| | | | | | | |
Collapse
|
10
|
Wang G, De J, Schoeniger JS, Roe DC, Carbonell RG. A hexamer peptide ligand that binds selectively to staphylococcal enterotoxin B: isolation from a solid phase combinatorial library. ACTA ACUST UNITED AC 2004; 64:51-64. [PMID: 15251031 DOI: 10.1111/j.1399-3011.2004.00170.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
By screening a solid-phase combinatorial peptide library, a short peptide ligand, YYWLHH, has been discovered that binds with high affinity and selectivity to staphylococcal enterotoxin B (SEB), but only weakly to other SEs that share sequence and structural homology with SEB. Using column affinity chromatography with an immobilized YYWLHH stationary phase, it was possible to separate SEB quantitatively from Staphylococcus aureus fermentation broth, a complex mixture of proteins, carbohydrates and other biomolecules. The immobilized peptide was also used to purify native SEB from a mixture containing denatured and hydrolyzed SEB, and showed little cross-reactivity with other SEs. To our knowledge this is the first report of a highly specific short peptide ligand for SEB. Such a ligand is a potential candidate to replace antibodies for detection, removal and purification strategies for SEB.
Collapse
Affiliation(s)
- G Wang
- Department of Chemical Engineering, North Carolina State University, 1017 Main Campus Drive, Centennial Campus, Partner's Building I, Suite 3200, Box 7006, Raleigh, NC 27695-7006, USA
| | | | | | | | | |
Collapse
|
11
|
Smith RG, Missailidis S, Price MR. Purification of anti-MUC1 antibodies by peptide mimotope affinity chromatography using peptides derived from a polyvalent phage display library. J Chromatogr B Analyt Technol Biomed Life Sci 2002; 766:13-26. [PMID: 11820288 DOI: 10.1016/s0378-4347(01)00422-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A polyvalent, lytic phage display system (T7Select415-1b) displaying a random peptide library has been investigated for its ability to discover novel mimotopes reactive with the therapeutic monoclonal antibody C595. Sequence analysis of enriched phage lead to the identification of a predominant sequence RNREAPRGKICS, and two other consensus sequences RXXP and RXP. The novel synthetic peptide RNREAPRGKICS was linked to beaded agarose and the performance as a mimotope affinity chromatography matrix evaluated. Antibody purified using the novel matrix was found to be of higher specific reactivity than antibody purified using the conventional epitope matrix (peptide APDTRPAPG). The RNREAPRGKICS peptide binding to C595 demonstrated a higher equilibrium association constant (K(A)=0.75 x 10(6)) than the epitope peptide (K(A)=0.16 x 10(6)). Circular dichroism showed that the novel peptide had a more highly ordered structure at 4 degrees C and room temperature, than the epitope peptide.
Collapse
Affiliation(s)
- Richard G Smith
- University of Nottingham, Cancer Research Laboratories, School of Pharmaceutical Sciences, UK.
| | | | | |
Collapse
|
12
|
Murray A, Smith RG, Brady K, Williams S, Badley RA, Price MR. Generation and refinement of peptide mimetic ligands for paratope-specific purification of monoclonal antibodies. Anal Biochem 2001; 296:9-17. [PMID: 11520027 DOI: 10.1006/abio.2001.5235] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Paratope-specific purification of antibodies has distinct advantages over conventional methods of antibody purification with respect to its capacity to isolate product of high purity and immunoreactivity. The present report addresses the problems of identifying peptide ligands for the purification of antibodies reactive with nonprotein antigens. Using an anti-steroid antibody as the model, a lead sequence that bound antibody was identified from a peptide phage display library. The minimum binding unit in this sequence was deduced using a series of truncated peptides synthesized on the heads of polyethylene pins. Replacement Net analysis of the minimum binding unit identified peptides with increased affinity for the antibody. The affinity-matured peptide mimotope bound antibody in solution. By molecular modeling the peptide was superimposable onto estrone-3-glucuronide localized in the crystal structure of the antibody binding pocket. In order to resolve problems of presentation posed by the reversal of orientation of the peptide on the affinity matrix compared with the pins, the mimotope peptide was synthesized in reverse sequence using d-amino acids. The resulting affinity matrix was effective for the purification of antibody. Eluted product demonstrated molecular homogeneity and high immunoreactivity. It is concluded that the combination of biological and chemical library techniques described provides a method for the generation and affinity maturation of mimotopes for antibodies against nonprotein antigens.
Collapse
Affiliation(s)
- A Murray
- Cancer Research Laboratories, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | | | | | | | | | | |
Collapse
|