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Cho CH, Kim JH, Kim J, Yun JW, Park TJ, Park JP. Re-engineering of peptides with high binding affinity to develop an advanced electrochemical sensor for colon cancer diagnosis. Anal Chim Acta 2020; 1146:131-139. [PMID: 33461708 DOI: 10.1016/j.aca.2020.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/17/2020] [Accepted: 11/07/2020] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) develops from polyps in the inner large intestine or rectum and an increasing incidence and high mortality rate has been observed in humans. Currently, colonoscopy is the preferred modality for early CRC diagnosis. However, this technique has several limitations, such as high medical costs and intricate procedures, leading to increasing demands for the development of a new, simple, and affordable diagnostic method. In this study, an advanced electrochemical biosensor based on rationally designed affinity peptides was developed for discriminating adenoma to carcinoma progression. Amino acid-substituted and rationally designed synthetic peptides (BP3-1 to BP3-8) based on in silico modeling studies were chemically synthesized, and covalently immobilized onto a gold electrode using aromatic ring compounds through surface chemistry techniques. The binding performance of the developed sensor system was observed using square wave voltammetry (SWV). The peptide BP3-2 was selected depending on its relative binding affinity; SWV indicated the limit of detection of BP3-2 for LRG1 to be 0.025 μg/mL. This sensor could distinguish the adenoma-carcinoma transition with improved binding abilities (specificity and selectivity), and stability in plasma samples spiked with LRG1 and real samples from patients with CRC. These results indicate that this electrochemical sensor system can be used for early monitoring of the colorectal adenoma to carcinoma progression.
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Affiliation(s)
- Chae Hwan Cho
- Department of Food Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Ji Hong Kim
- Department of Food Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Jayoung Kim
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Medicine, University of California Los Angeles, CA, 90095, USA
| | - Jong Won Yun
- Department of Biotechnology, Daegu University, Gyeongsan, 38453, Republic of Korea
| | - Tae Jung Park
- Department of Chemistry, Institute of Interdisciplinary Convergence Research, Research Institute of Chem-Bio Diagnostic Technology, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea.
| | - Jong Pil Park
- Department of Food Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea.
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2
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Ito M, Shimizu K, Honda H. Bile acid micelle disruption activity of short-chain peptides from tryptic hydrolyzate of edible proteins. J Biosci Bioeng 2020; 130:514-519. [DOI: 10.1016/j.jbiosc.2020.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/06/2020] [Accepted: 07/09/2020] [Indexed: 02/04/2023]
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Kozaki I, Suzuki T, You SC, Shimizu K, Honda H. Increasing the activity of cell adherent cyclic NGR peptides by optimizing the peptide length and amino acid character. J Pept Sci 2020; 27:e3287. [PMID: 32964600 DOI: 10.1002/psc.3287] [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] [Received: 05/15/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/17/2022]
Abstract
Cyclic peptides are an attractive modality for the development of therapeutics and the identification of functional cyclic peptides that contribute to novel drug development. The peptide array is one of the optimization methods for peptide sequences and also useful to understand sequence-function relationship of peptides. Cell adherent cyclic NGR peptide which selectively binds to the aminopeptidase N (APN or CD13) is known as an attractive tumor marker. In this study, we designed and screened a library of different length and an amino acid substitution library to identify stronger cell adhesion peptides and to reveal that the factor of higher binding between CD13 and optimized cyclic peptides. Additionally, we designed and evaluated 192 peptide libraries using eight representative amino acids to reduce the size of the library. Through these optimization steps of cyclic peptides, we identified 23 peptides that showed significantly higher cell adhesion activity than cKCNGRC, which was previously reported as a cell adhesion cyclic peptide. Among them, cCRHNGRARC showed the highest activity, that is, 1.65 times higher activity than cKCNGRC. An analysis of sequence and functional data showed that the rules which show higher cell adhesion activity for the three basic cyclic peptides (cCX1 HNGRHX2 C, cCX1 HNGRAX2 C, and cCX1 ANGRHX2 C) are related with the position of His residues and cationic amino acids.
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Affiliation(s)
- Ikko Kozaki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Takehiro Suzuki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Sheng-Chao You
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Kazunori Shimizu
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Hiroyuki Honda
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.,Innovative Research Center for Preventative Medical Engineering, Nagoya University, Nagoya, Japan
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Kozaki I, Shimizu K, Honda H. Disulfide linked hetero dimeric peptide arrays for screening functional peptides inside cells. J Biosci Bioeng 2020; 129:613-618. [DOI: 10.1016/j.jbiosc.2019.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/14/2019] [Accepted: 11/25/2019] [Indexed: 01/06/2023]
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Fluorescence-based Quantification of Bioactive Keratin Peptides from Feathers for Optimizing Large-scale Anaerobic Fermentation and Purification. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-018-0400-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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6
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Ito M, Shimizu K, Honda H. Searching for high-binding peptides to bile acid for inhibition of intestinal cholesterol absorption using principal component analysis. J Biosci Bioeng 2019; 127:366-371. [DOI: 10.1016/j.jbiosc.2018.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/23/2018] [Accepted: 08/13/2018] [Indexed: 01/17/2023]
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7
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Imai K, Shimizu K, Kamimura M, Honda H. Interaction between porous silica gel microcarriers and peptides for oral administration of functional peptides. Sci Rep 2018; 8:10971. [PMID: 30030485 PMCID: PMC6054636 DOI: 10.1038/s41598-018-29345-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/05/2018] [Indexed: 11/26/2022] Open
Abstract
Functional peptides, peptides that have biological activities, have attracted attention as active ingredients of functional foods and health foods. In particular, for food applications, because orally ingested peptides are degraded by digestive enzymes in the stomach, novel oral administration methods that can prevent peptide degradation and successfully deliver them intestinally are desired. In the present study, we focused on porous silica gel, which has many useful characteristics, such as large surface area, pH responsive functional groups, size controllable pores, and approval as food additives. We investigated the possibility of using porous silica gel as a peptide degradation protective microcarrier. As a result, we found that heat treatment of the silica gel at 600 °C for 2 h remarkably enhanced the adsorbed amount of many peptides under acidic conditions, and negatively charged and highly hydrophobic peptides had suitable characteristics for oral intestinal delivery with silica gel. Finally, we demonstrated the degree of protection from pepsin degradation and found that the protection of DFELEDD peptide was 57.1 ± 3.9% when DFELEDD was mixed with the heat-treated silica gel. These results indicated that the heat-treated silica gel is promising for efficient oral intestinal delivery of hydrophobic negatively charged peptides.
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Affiliation(s)
- Kento Imai
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Kazunori Shimizu
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Mitsuhiro Kamimura
- Fuji Silysia Chemical Ltd., 1846, 2-Chome, Kozoji-Cho, Kasugai-Shi, Aichi, 487-0013, Japan
| | - Hiroyuki Honda
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan.
- Innovative Research Center for Preventive Medical Engineering, Nagoya University, Nagoya, 464-8601, Japan.
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Zhu J, Wang Y, Li X, Han W, Zhao L. Understanding the interactions of different substrates with wild-type and mutant acylaminoacyl peptidase using molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:4285-4302. [PMID: 29235404 DOI: 10.1080/07391102.2017.1414634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Acylaminoacylpeptidase (AAP) belongs to peptidase protein family, which can degrade amyloid β-peptide forms in the brains of patients, and hence leads to Alzheimer's disease. And so, AAP is considered to be a novel target in the design of drugs against Alzheimer's disease. In this investigation, six molecular dynamics simulations were used to find that the interaction between the wild-type and R526V AAP with two different substrates (p-nitrophenylcaprylate and Ac-Leu-p-nitroanilide). Our results were as follows: firstly, Ac-Leu-p-nitroanilide bound to R526V AAP to form a more disordered loop (residues 552-562) in the α/β-hydrolase fold like of AAP, which caused an open and inactive AAP domain form, secondly, binding p-nitrophenylcaprylate and Ac-Leu-p-nitroanilide to AAP can decrease the flexibility of residues 225-250, 260-270, and 425-450, in which the ordered secondary structures may contain the suitable geometrical structure and so it is useful to serine attack. Our theoretical results showed that the binding of the two substrates can induce specific conformational changes responsible for the diverse AAP catalytic specificity. These theoretical substrate-induced structural diversities can help explain the abilities of AAPs to recognize and hydrolyze extremely different substrates.
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Affiliation(s)
- Jingxuan Zhu
- a Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences , Jilin University , 2699 Qianjin Street, Changchun 130012 , China
| | - Yan Wang
- b Department of General Surgery , China-Japan Union Hospital of Jilin University , Changchun , China
| | - Xin Li
- a Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences , Jilin University , 2699 Qianjin Street, Changchun 130012 , China
| | - Weiwei Han
- a Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences , Jilin University , 2699 Qianjin Street, Changchun 130012 , China
| | - Li Zhao
- a Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences , Jilin University , 2699 Qianjin Street, Changchun 130012 , China
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Kozaki I, Shimizu K, Honda H. Effective modification of cell death-inducing intracellular peptides by means of a photo-cleavable peptide array-based screening system. J Biosci Bioeng 2017; 124:209-214. [DOI: 10.1016/j.jbiosc.2017.03.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/22/2017] [Indexed: 10/19/2022]
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10
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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.
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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.
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