1
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Biyani M, Biyani M, Nishigaki K. Biomolecular display technology: a new tool for drug discovery. Anim Biotechnol 2020. [DOI: 10.1016/b978-0-12-811710-1.00019-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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2
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Kushwaha A, Takamura Y, Nishigaki K, Biyani M. Competitive non-SELEX for the selective and rapid enrichment of DNA aptamers and its use in electrochemical aptasensor. Sci Rep 2019; 9:6642. [PMID: 31040350 PMCID: PMC6491428 DOI: 10.1038/s41598-019-43187-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 04/17/2019] [Indexed: 02/07/2023] Open
Abstract
The SELEX (Systematic Evolution of Ligands by EXponential enrichment) method has been used successfully since 1990, but work is still required to obtain highly specific aptamers. Here, we present a novel approach called ‘Competitive non-SELEX’ (and termed as ‘SELCOS’ (Systematic Evolution of Ligands by COmpetitive Selection)) for readily obtaining aptamers that can discriminate between highly similar targets. This approach is based on the theoretical background presented here, in which under the co-presence of two similar targets, a specific binding type can be enriched more than a nonspecifically binding one during repetitive steps of partitioning with no PCR amplification between them. This principle was experimentally confirmed by the selection experiment for influenza virus subtype-specific DNA aptamers. Namely, the selection products (pools of DNA aptamers) obtained by SELCOS were subjected to a DEPSOR-mode electrochemical sensor, enabling the method to select subtype-specific aptamer pools. From the clonal analysis of these pools, only a few rounds of in vitro selection were sufficient to achieve the surprisingly rapid enrichment of a small number of aptamers with high selectivity, which could be attributed to the SELCOS principle and the given selection pressure program. The subtype-specific aptamers obtained in this manner had a high affinity (e.g., KD = 82 pM for H1N1; 88 pM for H3N2) and negligible cross-reactivity. By making the H1N1-specific DNA aptamer a sensor unit of the DEPSOR electrochemical detector, an influenza virus subtype-specific and portable detector was readily constructed, indicating how close it is to the field application goal.
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Affiliation(s)
- Ankita Kushwaha
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
| | - Yuzuru Takamura
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
| | - Koichi Nishigaki
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan.,BioSeeds Corporation, JAIST venture business laboraotry, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
| | - Manish Biyani
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan. .,BioSeeds Corporation, JAIST venture business laboraotry, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan.
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Sharma K, Hongo A, Nishigaki K, Takamura Y, Biyani M. 'Head-to-Head' mRNA display for the translation of multi-copied proteins with a free C-terminus. Anal Biochem 2018; 557:77-83. [PMID: 30031739 DOI: 10.1016/j.ab.2018.07.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/14/2018] [Accepted: 07/17/2018] [Indexed: 12/01/2022]
Abstract
With the development of various methods for affinity-based selection of proteins such as phage display, ribosomal display, and mRNA display, the progress in this field has been gradually shifting to function-based selection, such as through single-molecule observation, genetic selection, and compartmentalization technologies. In this vein, we present an opposite link mode of mRNA display termed as a 'Head-to-Head' (H2H) link. The key technique in H2H, formation of a covalent bond between O6-benzylguanine (BG) and O6-alkylguanine-DNA alkyltransferase (AGT), was demonstrated to be workable in H2H ligation, where mRNA is linked to a nascent AGT via a BG-DNA linker, resulting in a "(C-terminus) protein-BG-DNA linker-mRNA (5'-terminus)" conjugate. Thus, a head (N-terminus) to head (5'-terminus) linkage is formed. Among the advantages of H2H, the generation of multi-copied proteins is the most promising and was proven to be possible owing to the restored stop codon, which had been intentionally removed in the conventional mRNA display. Another advantage is obviously having a free C-terminus of the protein, which can be used for modifications such as C-terminal methylation, α-amidation, and others, which occur in nature. A superior merit of H2H is that it makes it possible to use a single construct commonly in mRNA display (affinity-based) and compartmentalization technologies (function-based) without requiring complicated construct changes.
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Affiliation(s)
- Kirti Sharma
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi city, Ishikawa 923-1292, Japan
| | - Aya Hongo
- Graduate School of Science and Technology, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama city, Saitama 338-8570, Japan
| | - Koichi Nishigaki
- Graduate School of Science and Technology, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama city, Saitama 338-8570, Japan; Center for Single Nanoscale Innovative Devices, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi city, Ishikawa 923-1292, Japan; BioSeeds Corporation, JAIST venture business laboratory, 1-1 Asahidai, Nomi city, Ishikawa 923-1292, Japan
| | - Yuzuru Takamura
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi city, Ishikawa 923-1292, Japan; Center for Single Nanoscale Innovative Devices, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi city, Ishikawa 923-1292, Japan
| | - Manish Biyani
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi city, Ishikawa 923-1292, Japan; Center for Single Nanoscale Innovative Devices, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi city, Ishikawa 923-1292, Japan; BioSeeds Corporation, JAIST venture business laboratory, 1-1 Asahidai, Nomi city, Ishikawa 923-1292, Japan.
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4
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Tung NT, Tue PT, Thi Ngoc Lien T, Ohno Y, Maehashi K, Matsumoto K, Nishigaki K, Biyani M, Takamura Y. Peptide aptamer-modified single-walled carbon nanotube-based transistors for high-performance biosensors. Sci Rep 2017; 7:17881. [PMID: 29263412 PMCID: PMC5738443 DOI: 10.1038/s41598-017-18169-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/05/2017] [Indexed: 11/09/2022] Open
Abstract
Biosensors employing single-walled carbon nanotube field-effect transistors (SWCNT FETs) offer ultimate sensitivity. However, besides the sensitivity, a high selectivity is critically important to distinguish the true signal from interference signals in a non-controlled environment. This work presents the first demonstration of the successful integration of a novel peptide aptamer with a liquid-gated SWCNT FET to achieve highly sensitive and specific detection of Cathepsin E (CatE), a useful prognostic biomarker for cancer diagnosis. Novel peptide aptamers that specifically recognize CatE are engineered by systemic in vitro evolution. The SWCNTs were firstly grown using the thermal chemical vapor deposition (CVD) method and then were employed as a channel to fabricate a SWCNT FET device. Next, the SWCNTs were functionalized by noncovalent immobilization of the peptide aptamer using 1-pyrenebutanoic acid succinimidyl ester (PBASE) linker. The resulting FET sensors exhibited a high selectivity (no response to bovine serum albumin and cathepsin K) and label-free detection of CatE at unprecedentedly low concentrations in both phosphate-buffered saline (2.3 pM) and human serum (0.23 nM). Our results highlight the use of peptide aptamer-modified SWCNT FET sensors as a promising platform for near-patient testing and point-of-care testing applications.
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Affiliation(s)
- Nguyen Thanh Tung
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi city, Ishikawa, 923-1292, Japan
| | - Phan Trong Tue
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi city, Ishikawa, 923-1292, Japan
| | - Truong Thi Ngoc Lien
- School of Engineering Physics, Hanoi University of Science and Technology, 1 Dai Co Viet Road, Hanoi, Vietnam
| | - Yasuhide Ohno
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-4 Shinkuracho, Tokushima, 770-8501, Japan
| | - Kenzo Maehashi
- Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo, 184-8588, Japan
| | - Kazuhiko Matsumoto
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Koichi Nishigaki
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi city, Ishikawa, 923-1292, Japan.,Department of Functional Materials Science, Saitama University, 255 Shimo-okubo Sakura-ku, Saitama city, Saitama, 338-8570, Japan
| | - Manish Biyani
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi city, Ishikawa, 923-1292, Japan. .,Center for Single Nanoscale Innovative Devices, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, 923-1292, Japan.
| | - Yuzuru Takamura
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi city, Ishikawa, 923-1292, Japan. .,Center for Single Nanoscale Innovative Devices, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, 923-1292, Japan.
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Mengwasser J, Babes L, Cordes S, Mertlitz S, Riesner K, Shi Y, McGearey A, Kalupa M, Reinheckel T, Penack O. Cathepsin E Deficiency Ameliorates Graft-versus-Host Disease and Modifies Dendritic Cell Motility. Front Immunol 2017; 8:203. [PMID: 28298913 PMCID: PMC5331043 DOI: 10.3389/fimmu.2017.00203] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/14/2017] [Indexed: 01/15/2023] Open
Abstract
Microbial products influence immunity after allogeneic hematopoietic stem cell transplantation (allo-SCT). In this context, the role of cathepsin E (Ctse), an aspartate protease known to cleave bacterial peptides for antigen presentation in dendritic cells (DCs), has not been studied. During experimental acute graft-versus-host disease (GVHD), we found infiltration by Ctse-positive immune cells leading to higher Ctse RNA- and protein levels in target organs. In Ctse-deficient allo-SCT recipients, we found ameliorated GVHD, improved survival, and lower numbers of tissue-infiltrating DCs. Donor T cell proliferation was not different in Ctse-deficient vs. wild-type allo-SCT recipients in MHC-matched and MHC-mismatched models. Furthermore, Ctse-deficient DCs had an intact ability to induce allogeneic T cell proliferation, suggesting that its role in antigen presentation may not be the main mechanism how Ctse impacts GVHD. We found that Ctse deficiency significantly decreases DC motility in vivo, reduces adhesion to extracellular matrix (ECM), and diminishes invasion through ECM. We conclude that Ctse has a previously unrecognized role in regulating DC motility that possibly contributes to reduced DC counts and ameliorated inflammation in GVHD target organs of Ctse-deficient allo-SCT recipients. However, our data do not provide definite proof that the observed effect of Ctse−/− deficiency is exclusively mediated by DCs. A contribution of Ctse−/−-mediated functions in other recipient cell types, e.g., macrophages, cannot be excluded.
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Affiliation(s)
- Jörg Mengwasser
- Medical Department, Division of Hematology, Oncology and Tumor Immunology, Charité University Medicine , Berlin , Germany
| | - Liane Babes
- Faculty of Medicine, BIOSS Centre for Biological Signalling Studies, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg , Freiburg , Germany
| | - Steffen Cordes
- Medical Department, Division of Hematology, Oncology and Tumor Immunology, Charité University Medicine , Berlin , Germany
| | - Sarah Mertlitz
- Medical Department, Division of Hematology, Oncology and Tumor Immunology, Charité University Medicine , Berlin , Germany
| | - Katarina Riesner
- Medical Department, Division of Hematology, Oncology and Tumor Immunology, Charité University Medicine , Berlin , Germany
| | - Yu Shi
- Medical Department, Division of Hematology, Oncology and Tumor Immunology, Charité University Medicine , Berlin , Germany
| | - Aleixandria McGearey
- Medical Department, Division of Hematology, Oncology and Tumor Immunology, Charité University Medicine , Berlin , Germany
| | - Martina Kalupa
- Medical Department, Division of Hematology, Oncology and Tumor Immunology, Charité University Medicine , Berlin , Germany
| | - Thomas Reinheckel
- Faculty of Medicine, BIOSS Centre for Biological Signalling Studies, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg , Freiburg , Germany
| | - Olaf Penack
- Medical Department, Division of Hematology, Oncology and Tumor Immunology, Charité University Medicine , Berlin , Germany
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6
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Hayakawa Y, Matsuno M, Tanaka M, Wada A, Kitamura K, Takei O, Sasaki R, Mizukami T, Hasegawa M. Complementary DNA display selection of high-affinity peptides binding the vacuolating toxin (VacA) of Helicobacter pylori. J Pept Sci 2015; 21:710-6. [PMID: 26152929 DOI: 10.1002/psc.2795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 05/24/2015] [Accepted: 05/27/2015] [Indexed: 11/06/2022]
Abstract
Artificial peptides designed for molecular recognition of a bacterial toxin have been developed. Vacuolating cytotoxin A protein (VacA) is a major virulence factor of Helicobacter pylori, a gram-negative microaerophilic bacterium inhabiting the upper gastrointestinal tract, particularly the stomach. This study attempted to identify specific peptide sequences with high affinity for VacA using systematic directed evolution in vitro, a cDNA display method. A surface plasmon resonance-based biosensor and fluorescence correlation spectroscopy to examine binding of peptides with VacA identified a peptide (GRVNQRL) with high affinity. Cyclization of the peptide by attaching cysteine residues to both termini improved its binding affinity to VacA, with a dissociation constant (Kd ) of 58 nm. This study describes a new strategy for the development of artificial functional peptides, which are promising materials in biochemical analyses and medical applications.
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Affiliation(s)
- Yumiko Hayakawa
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura 1266, Nagahama, Shiga, 526-0829, Japan
| | - Mitsuhiro Matsuno
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura 1266, Nagahama, Shiga, 526-0829, Japan
| | - Makoto Tanaka
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura 1266, Nagahama, Shiga, 526-0829, Japan
| | - Akihiro Wada
- Institute for Tropical Medicine, Nagasaki University, Sakamoto 1-12-4, Nagasaki, 852-8523, Japan
| | - Koichiro Kitamura
- JANUSYS Co., Ltd., Kamiaoki 3-12-18-508, Kawaguchi, Saitama, 333-0844, Japan
| | - Osamu Takei
- Lifetech Co., Ltd., Miyadera 4074, Iruma, Saitama, 358-0014, Japan
| | - Ryuzo Sasaki
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura 1266, Nagahama, Shiga, 526-0829, Japan
| | - Tamio Mizukami
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura 1266, Nagahama, Shiga, 526-0829, Japan
| | - Makoto Hasegawa
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura 1266, Nagahama, Shiga, 526-0829, Japan
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7
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Ghimire Gautam S, Komatsu M, Nishigaki K. Strong Inhibition of Beta-Amyloid Peptide Aggregation Realized by Two-Steps Evolved Peptides. Chem Biol Drug Des 2014; 85:356-68. [DOI: 10.1111/cbdd.12400] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 07/12/2014] [Accepted: 07/21/2014] [Indexed: 12/24/2022]
Affiliation(s)
- Sunita Ghimire Gautam
- Department of Functional Materials Science; Graduate School of Science and Engineering; Saitama University; 255 Shimo-okubo Sakura-Ku Saitama-Shi 338-8570 Japan
| | - Masayuki Komatsu
- Department of Functional Materials Science; Graduate School of Science and Engineering; Saitama University; 255 Shimo-okubo Sakura-Ku Saitama-Shi 338-8570 Japan
| | - Koichi Nishigaki
- Department of Functional Materials Science; Graduate School of Science and Engineering; Saitama University; 255 Shimo-okubo Sakura-Ku Saitama-Shi 338-8570 Japan
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8
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Biomolecular Display Technology. Anim Biotechnol 2014. [DOI: 10.1016/b978-0-12-416002-6.00020-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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9
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Peptide-Modulated Activity Enhancement of Acidic Protease Cathepsin E at Neutral pH. INTERNATIONAL JOURNAL OF PEPTIDES 2012; 2012:316432. [PMID: 23365585 PMCID: PMC3534310 DOI: 10.1155/2012/316432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/20/2012] [Accepted: 10/27/2012] [Indexed: 11/17/2022]
Abstract
Enzymes are regulated by their activation and inhibition. Enzyme activators can often be effective tools for scientific and medical purposes, although they are more difficult to obtain than inhibitors. Here, using the paired peptide method, we report on protease-cathepsin-E-activating peptides that are obtained at neutral pH. These selected peptides also underwent molecular evolution, after which their cathepsin E activation capability improved. Thus, the activators we obtained could enhance cathepsin-E-induced cancer cell apoptosis, which indicated their potential as cancer drug precursors.
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10
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Kitamura K, Komatsu M, Biyani M, Futakami M, Kawakubo T, Yamamoto K, Nishigaki K. Proven in vitro evolution of protease cathepsin E-inhibitors and -activators at pH 4.5 using a paired peptide method. J Pept Sci 2012; 18:711-9. [PMID: 23109368 DOI: 10.1002/psc.2453] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 07/08/2012] [Accepted: 08/20/2012] [Indexed: 12/25/2022]
Abstract
Improving a particular function of molecules is often more difficult than identifying such molecules ab initio. Here, a method to acquire higher affinity and/or more functional peptides was developed as a progressive library selection method. The primary library selection products were utilized to build a secondary library composed of blocks of 4 amino acids, of which selection led to peptides with increased activity. These peptides were further converted to randomly generate paired peptides. Cathepsin E-inhibitors thus obtained exhibited the highest activities and affinities (pM order). This was also the case with cathepsin E-activating peptides, proving the methodological effectiveness. The primary, secondary, and tertiary library selections can be regarded as module-finding, module-shuffling, and module-pairing, respectively, which resembles the progression of the natural evolution of proteins. The mode of peptide binding to their target proteins is discussed in analogy to antibodies and epitopes of an antigen.
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Affiliation(s)
- Koichiro Kitamura
- Janusys Corporation, #508, Saitama Industrial Technology Center, 3-12-18 Kami-Aoki, Kawaguchi, Saitama, 333-0844, Japan; Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama, 338-8570, Japan; Rational Evolutionary Design of Advanced Biomolecules, Saitama (REDS), Saitama Small Enterprise Promotion Corporation, #552, Saitama Industrial Technology Center, 3-12-18 Kami-Aoki, Kawaguchi, Saitama, 333-0844, Japan; City Area Program Saitama Metropolitan Area, Saitama small and medium Enterprises Development Corporation, 2-3-2 Kamiochiai, Chuo-ku, Saitama City, Saitama, 338-0001, Japan
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11
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In vitro selection of a peptide antagonist of growth hormone secretagogue receptor using cDNA display. Proc Natl Acad Sci U S A 2012; 109:11121-6. [PMID: 22723348 DOI: 10.1073/pnas.1203561109] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are major drug targets, and their ligands are currently being explored and developed by many pharmaceutical companies and independent researchers. Class A (rhodopsin-like) GPCRs compose a predominant GPCR family; therefore, class A GPCR ligands are in demand. Growth hormone secretagogue receptor (GHS-R) is a class A GPCR that stimulates food intake by binding to its peptide ligand, ghrelin. Therefore, antagonists of GHS-R are expected to exert antiobesity function. In this article, we describe the use of cDNA display to screen for successfully and identify an antagonistic peptide of GHS-R. The antagonistic peptide inhibited the ghrelin-induced increase in intracellular Ca(2+) in vitro (IC(50) = approximately 10 μM) and repressed the contraction of isolated animal stomach in response to ghrelin. Furthermore, peripheral administration of the peptide inhibited the food intake of mice. This work provides new insight into the development of antiobesity drugs and describes a method for the discovery of unique peptide ligands for class A GPCRs.
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Nemoto N, Tsutsui C, Yamaguchi J, Ueno S, Machida M, Kobayashi T, Sakai T. Antagonistic effect of disulfide-rich peptide aptamers selected by cDNA display on interleukin-6-dependent cell proliferation. Biochem Biophys Res Commun 2012; 421:129-33. [DOI: 10.1016/j.bbrc.2012.03.130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 03/26/2012] [Indexed: 10/28/2022]
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13
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Aita T, Husimi Y. Toward an evolutionary containment of evolving pathogen-receptors by using an ensemble of multiple mutant ligands: from the viewpoint of fitness landscape in sequence space. J Theor Biol 2011; 296:49-55. [PMID: 22172531 DOI: 10.1016/j.jtbi.2011.11.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Revised: 11/28/2011] [Accepted: 11/30/2011] [Indexed: 11/18/2022]
Abstract
It is known that even if a ligand peptide is designed to bind to a target receptor on the surface of a pathogen such as viruses, bacteria or cancer cells, it is likely that some receptors are subject to random mutation and thus the ligand has a reduced ability to bind to these receptors. This issue is known as drug-resistant or escape mutants. In this paper, we present an idea to inhibit the evolving receptors by using an ensemble of all possible single- or double-point mutant sequences of the ligand peptide. Several mutant ligands in the ensemble are expected to bind to the mutant receptors, and then the ensemble may create a defensive wall surrounding the target receptors in receptor-sequence space. We examined the effectiveness of this "evolutionary containment" of the evolving receptors through eight peptide-protein complex systems, which were retrieved from the Protein Data Bank (PDB). As a result, we obtained a suggestion that the original (or parent) ligand sequence should be designed to have as high fitness as possible but to be not local optima, in order to maximize the rate of the evolutionary containment. This may be a strategy of the drug-design against evolving pathogens.
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Affiliation(s)
- Takuyo Aita
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan.
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14
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Matarrese P, Nencioni L, Checconi P, Ciarlo L, Gambardella L, Ascione B, Sgarbanti R, Garaci E, Malorni W, Palamara AT. Pepstatin A alters host cell autophagic machinery and leads to a decrease in influenza A virus production. J Cell Physiol 2011; 226:3368-77. [DOI: 10.1002/jcp.22696] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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15
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Biyani M, Futakami M, Kitamura K, Kawakubo T, Suzuki M, Yamamoto K, Nishigaki K. In Vitro Selection of Cathepsin E-Activity-Enhancing Peptide Aptamers at Neutral pH. INTERNATIONAL JOURNAL OF PEPTIDES 2011; 2011:834525. [PMID: 21527983 PMCID: PMC3064998 DOI: 10.1155/2011/834525] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 01/17/2011] [Indexed: 12/14/2022]
Abstract
The aspartic protease cathepsin E has been shown to induce apoptosis in cancer cells under physiological conditions. Therefore, cathepsin E-activity-enhancing peptides functioning in the physiological pH range are valuable potential cancer therapeutic candidates. Here, we have used a general in vitro selection method (evolutionary rapid panning analysis system (eRAPANSY)), based on inverse substrate-function link (SF-link) selection to successfully identify cathepsin E-activity-enhancing peptide aptamers at neutral pH. A successive enrichment of peptide activators was attained in the course of selection. One such peptide activated cathepsin E up to 260%, had a high affinity (K(D); ∼300 nM), and had physiological activity as demonstrated by its apoptosis-inducing reaction in cancerous cells. This method is expected to be widely applicable for the identification of protease-activity-enhancing peptide aptamers.
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Affiliation(s)
- Madhu Biyani
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Saitama 338-8570, Japan
- City Area Program Saitama Metropolitan Area, Saitama Small and Medium Enterprises Development Corporation, 2-3-2 Kamiochiai, Chuo-Ku, Saitama 338-0001, Japan
| | - Masae Futakami
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Saitama 338-8570, Japan
- City Area Program Saitama Metropolitan Area, Saitama Small and Medium Enterprises Development Corporation, 2-3-2 Kamiochiai, Chuo-Ku, Saitama 338-0001, Japan
| | - Koichiro Kitamura
- City Area Program Saitama Metropolitan Area, Saitama Small and Medium Enterprises Development Corporation, 2-3-2 Kamiochiai, Chuo-Ku, Saitama 338-0001, Japan
- Rational Evolutionary Design of Advanced Biomolecules, Saitama (REDS) Group, Saitama Small Enterprise Promotion Corporation, no. 552 Saitama Industrial Technology Center, 3-12-18 Kami-Aoki, Kawaguchi, Saitama 333-0844, Japan
- Janusys Corporation, no. 508 Saitama Industrial Technology Center, 3-12-18 Kami-Aoki, Kawaguchi, Saitama 333-0844, Japan
| | - Tomoyo Kawakubo
- Proteolysis Research Laboratory, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Miho Suzuki
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Saitama 338-8570, Japan
| | - Kenji Yamamoto
- Rational Evolutionary Design of Advanced Biomolecules, Saitama (REDS) Group, Saitama Small Enterprise Promotion Corporation, no. 552 Saitama Industrial Technology Center, 3-12-18 Kami-Aoki, Kawaguchi, Saitama 333-0844, Japan
- Proteolysis Research Laboratory, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Koichi Nishigaki
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Saitama 338-8570, Japan
- City Area Program Saitama Metropolitan Area, Saitama Small and Medium Enterprises Development Corporation, 2-3-2 Kamiochiai, Chuo-Ku, Saitama 338-0001, Japan
- Rational Evolutionary Design of Advanced Biomolecules, Saitama (REDS) Group, Saitama Small Enterprise Promotion Corporation, no. 552 Saitama Industrial Technology Center, 3-12-18 Kami-Aoki, Kawaguchi, Saitama 333-0844, Japan
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Abstract
We developed a method for selective purification of DNA using the cationic detergent, cetyltrimethylammonium bromide (CTAB), accompanied with urea and controlled high-salt (NaCl) concentration. This method is effective for rapid separation of DNA fragments from artifacts such as PCR primer dimers or ligation adapters. The CTAB-associated purification completely removed the short PCR artifacts and primers, as well as enzymes and buffer, while recovering a sufficient quantity of amplicons for subsequent experiments such as preparation of libraries. This method could also be applied to the fractionation of nucleic acids generated by other types of reactions.
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Kinoshita Y, Tayama T, Kitamura K, Salimullah M, Uchida H, Suzuki M, Husimi Y, Nishigaki K. Novel concept microarray enabling PCR and multistep reactions through pipette-free aperture-to-aperture parallel transfer. BMC Biotechnol 2010; 10:71. [PMID: 20923572 PMCID: PMC2959086 DOI: 10.1186/1472-6750-10-71] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Accepted: 10/06/2010] [Indexed: 11/15/2022] Open
Abstract
Background The microarray has contributed to developing the omic analysis. However, as it depends basically on the surface reaction, it is hard to perform bulk reactions and sequential multistep reactions. On the other hand, the popular microplate technology, which has a great merit of being able to perform parallel multistep reactions, has come to its limit in increasing the number of wells (currently, up to 9600) and reducing the volume to deal with due to the difficulty in operations. Results Here, we report a novel microarray technology which enables us to explore advanced applications, termed microarray-with-manageable volumes (MMV). The technical essence is in the pipette-free direct parallel transfer from well to well performed by centrifugation, evading the evaporation and adsorption-losses during handling. By developing the MMV plate, accompanying devices and techniques, generation of multiple conditions (256 kinds) and performance of parallel multistep reactions, including PCR and in vitro translation reactions, have been made possible. These were demonstrated by applying the MMV technology to searching lysozyme-crystallizing conditions and selecting peptides aimed for Aβ-binding or cathepsin E-inhibition. Conclusions With the introduction of a novel concept microarray (MMV) technology, parallel and multistep reactions in sub-μL scale have become possible.
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Affiliation(s)
- Yasunori Kinoshita
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama 338-8570, Japan
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Selective detection of Cathepsin E proteolytic activity. Biochim Biophys Acta Gen Subj 2010; 1800:1002-8. [PMID: 20600629 DOI: 10.1016/j.bbagen.2010.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 05/03/2010] [Accepted: 06/11/2010] [Indexed: 11/21/2022]
Abstract
BACKGROUND Aspartic proteases Cathepsin (Cath) E and D are two different proteases, but they share many common characteristics, including molecular weight, catalytic mechanism, substrate preferences, proteolytic conditions and inhibition susceptibility. To define the biological roles of these proteases, it is necessary to elucidate their substrate specificity. In the present study, we report a new peptide-substrate that is only sensitive to Cath E but not Cath D. METHODS Substrate e, Mca-Ala-Gly-Phe-Ser-Leu-Pro-Ala-Lys(Dnp)-DArg-CONH₂, designed in such a way that due to the close proximity of a Mca-donor and a Dnp-acceptor, near complete intramolecular quenching effect was achieved in its intact state. After the proteolytic cleavage of the hydrophobic motif of peptide substrate, both Mca and Dnp would be further apart, resulting in bright fluorescence. RESULTS Substrate e showed a 265 fold difference in the net fluorescence signals between Cath E and D. This Cath E selectivity was established by having -Leu**Pro- residues at the scissile peptide bond. The confined cleavage site of substrate e was confirmed by LC-MS. The catalytic efficiency (K(cat)/K(M)) of Cath E for substrate e was 16.7 μM⁻¹S⁻¹. No measurable catalytic efficiency was observed using Cath D and no detectable fluorescent changes when incubated with Cath S and Cath B. CONCLUSIONS This study demonstrated the promise of using the developed fluorogenic substrate e as a selective probe for Cath E proteolytic activity measurement. GENERAL SIGNIFICANCE This study forms the foundation of Cath E specific inhibitor development in further studies.
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Aita T, Nishigaki K, Husimi Y. Toward the fast blind docking of a peptide to a target protein by using a four-body statistical pseudo-potential. Comput Biol Chem 2010; 34:53-62. [DOI: 10.1016/j.compbiolchem.2009.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Revised: 09/27/2009] [Accepted: 10/20/2009] [Indexed: 11/26/2022]
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