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Yuan Y, Li Y, Liu S, Gong P, Lin J, Zhang X. An overview of aptamer: Design strategy, prominent applications, and potential challenge in plants. J Plant Physiol 2024; 296:154235. [PMID: 38531181 DOI: 10.1016/j.jplph.2024.154235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/29/2024] [Accepted: 03/17/2024] [Indexed: 03/28/2024]
Abstract
Aptamers, serving as highly efficient molecular recognition and biotechnology tools, have garnered increasing interest in the realm of plant science in recent years. Aptamers are synthetic single-stranded short nucleotides or peptides, that bind targets with high specificity and affinity, triggering precise biological responses. As an alternative to antibodies, aptamers present promising avenues for advancement in biological researches. Aptamers function in a range of fields, encompassing cell signaling, drug development, biosensor technology, as well as botany, agricultural and forestry sciences. In this review, we introduce classifications and screening methods of aptamers, as well as aptamer-based technologies, highlighting their significant contributions to recent advancements. With their powerful functionality and ability to bind targets with high specificity and affinity, aptamers offer promising opportunities for breakthroughs in plant research.
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Affiliation(s)
- Yanhui Yuan
- State Key Laboratory of Tree Genetics and Breeding, State Key Laboratory of Efficient Production of Forest Resources, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China; Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, 100083, China
| | - Yi Li
- State Key Laboratory of Tree Genetics and Breeding, State Key Laboratory of Efficient Production of Forest Resources, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China; Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, 100083, China
| | - Siying Liu
- State Key Laboratory of Tree Genetics and Breeding, State Key Laboratory of Efficient Production of Forest Resources, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Pichang Gong
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Jinxing Lin
- State Key Laboratory of Tree Genetics and Breeding, State Key Laboratory of Efficient Production of Forest Resources, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China; Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, 100083, China
| | - Xi Zhang
- State Key Laboratory of Tree Genetics and Breeding, State Key Laboratory of Efficient Production of Forest Resources, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China; Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing, 100083, China.
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2
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Liu T, Gao C, Wang J, Song J, Chen X, Chen H, Zhao X, Tang H, Gu D. Peptide aptamer-based time-resolved fluoroimmunoassay for CHIKV diagnosis. Virol J 2023; 20:166. [PMID: 37501131 PMCID: PMC10375649 DOI: 10.1186/s12985-023-02132-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/17/2023] [Indexed: 07/29/2023] Open
Abstract
BACKGROUND Chikungunya virus (CHIKV) and Dengue virus (DENV) have similar clinical symptoms, which often induce misdiagnoses. Therefore, an antigen detection diagnostic system that can clearly identify these two viruses is desirable. METHODS In this study, we developed a novel peptide with high affinity and specificity to CHIKV, and further constructed peptide aptamer-based TRFIA assay to efficiently detect CHIKV. Peptide aptamer B2 (ITPQSSTTEAEL) and B3 (DTQGSNWI) were obtained through computer-aided design and selected as CHIKV-specific peptide aptamers based on their high binding affinity, strong hydrogen bonding, and RMSD of molecular docking. Then, a sandwich-Time-Resolved Fluoroimmunoassay (TRFIA) was successfully constructed for the detection of the interaction between peptide aptamers and viruses. RESULTS When using B2 as the detection element, highly specific detection of CHIKV E2 was achieved with detection limits of 8.5 ng/ml in PBS solution. Variation coefficient between inter-assay showed the disturbances received from the detection of clinical fluid specimens (including serum and urine), were also within acceptable limits. The detection limits for 10-fold dilution serum and urine were 57.8 ng/mL and 147.3 ng/mL, respectively. The fluorescent signal intensity exhibited a good linear correlation with E2 protein concentration in the range of 0-1000 ng/mL, indicating the potential for quantitative detection of E2 protein. CONCLUSIONS These results demonstrate that the construction of peptide aptamers with high affinity and specificity provides an excellent method for rapid diagnostic element screening, and the developed peptide aptamer B2 contributed to better detection of CHIKV viral particles compared to traditional antibodies.
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Affiliation(s)
- Tonggong Liu
- Department of Laboratory Medicine, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, 518035, Shenzhen, China
- School of Public Health, Dongguan Key Laboratory of Environmental Medicine, Guangdong Medical University, 523808, Guangdong, China
| | - Cheng Gao
- Department of Laboratory Medicine, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, 518035, Shenzhen, China
| | - Jingzhe Wang
- Department of Laboratory Medicine, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, 518035, Shenzhen, China
| | - Jianning Song
- Guangzhou Medical University, 510182, Guangzhou, China
| | - Xi Chen
- School of Public Health, Dongguan Key Laboratory of Environmental Medicine, Guangdong Medical University, 523808, Guangdong, China
| | - Hongfang Chen
- School of Public Health, Dongguan Key Laboratory of Environmental Medicine, Guangdong Medical University, 523808, Guangdong, China
| | - Xiaona Zhao
- Guangxi University of Chinese Medicine, 530004, Nanning, China
| | - Huanwen Tang
- School of Public Health, Dongguan Key Laboratory of Environmental Medicine, Guangdong Medical University, 523808, Guangdong, China.
| | - Dayong Gu
- Department of Laboratory Medicine, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, 518035, Shenzhen, China.
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Ali T, Klein AN, Vu A, Arifin MI, Hannaoui S, Gilch S. Peptide aptamer targeting Aβ-PrP-Fyn axis reduces Alzheimer's disease pathologies in 5XFAD transgenic mouse model. Cell Mol Life Sci 2023; 80:139. [PMID: 37149826 PMCID: PMC10164677 DOI: 10.1007/s00018-023-04785-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 04/11/2023] [Accepted: 04/22/2023] [Indexed: 05/08/2023]
Abstract
Currently, no effective therapeutics exist for the treatment of incurable neurodegenerative diseases such as Alzheimer's disease (AD). The cellular prion protein (PrPC) acts as a high-affinity receptor for amyloid beta oligomers (AβO), a main neurotoxic species mediating AD pathology. The interaction of AβO with PrPC subsequently activates Fyn tyrosine kinase and neuroinflammation. Herein, we used our previously developed peptide aptamer 8 (PA8) binding to PrPC as a therapeutic to target the AβO-PrP-Fyn axis and prevent its associated pathologies. Our in vitro results indicated that PA8 prevents the binding of AβO with PrPC and reduces AβO-induced neurotoxicity in mouse neuroblastoma N2a cells and primary hippocampal neurons. Next, we performed in vivo experiments using the transgenic 5XFAD mouse model of AD. The 5XFAD mice were treated with PA8 and its scaffold protein thioredoxin A (Trx) at a 14.4 µg/day dosage for 12 weeks by intraventricular infusion through Alzet® osmotic pumps. We observed that treatment with PA8 improves learning and memory functions of 5XFAD mice as compared to Trx-treated 5XFAD mice. We found that PA8 treatment significantly reduces AβO levels and Aβ plaques in the brain tissue of 5XFAD mice. Interestingly, PA8 significantly reduces AβO-PrP interaction and its downstream signaling such as phosphorylation of Fyn kinase, reactive gliosis as well as apoptotic neurodegeneration in the 5XFAD mice compared to Trx-treated 5XFAD mice. Collectively, our results demonstrate that treatment with PA8 targeting the AβO-PrP-Fyn axis is a promising and novel approach to prevent and treat AD.
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Affiliation(s)
- Tahir Ali
- Calgary Prion Research Unit, Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
- Cumming School of Medicine, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Antonia N Klein
- Calgary Prion Research Unit, Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
- Cumming School of Medicine, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Alex Vu
- Calgary Prion Research Unit, Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
- Cumming School of Medicine, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Maria I Arifin
- Calgary Prion Research Unit, Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
- Cumming School of Medicine, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Samia Hannaoui
- Calgary Prion Research Unit, Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
- Cumming School of Medicine, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Sabine Gilch
- Calgary Prion Research Unit, Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada.
- Cumming School of Medicine, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada.
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Xu Z, Jiang X, Li Y, Ma X, Tang Y, Li H, Yi K, Li J, Liu Z. Antifungal activity of montmorillonite/ peptide aptamer nanocomposite against Colletotrichum gloeosporioides on Stylosanthes. Int J Biol Macromol 2022; 217:282-290. [PMID: 35835303 DOI: 10.1016/j.ijbiomac.2022.07.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/20/2022] [Accepted: 07/05/2022] [Indexed: 11/30/2022]
Abstract
Chemical agents are effective treatment methods for anthracnose induced by pathogenic Colletotrichum gloeosporioides on Stylosanthes. However, excess consumption of chemical agents destroys the environment, synthetic biology was capable of conquering the issue. The antifungal agent is developed by enclosing a bio-synthesized peptide aptamer with layered montmorillonite via electrostatic interaction. Compared with free peptide aptamer, the nanocomposite exhibits higher antifungal activity against Colletotrichum gloeosporioides, further improving the utilization of peptide aptamer. The nanocomposite killed Colletotrichum gloeosporioides by releasing peptide aptamer after they entered the spore. Moreover, montmorillonite enhances the adhesion ability of peptide aptamer via hydrophobic interactions between nanomaterials and leaves, prolonging the extension time of nanocomposite on leaves. Consequently, 0.1 mg of nanocomposite demonstrates a comparable effect to commercial carbendazim (1 %) to prevent anthracnose on leaves of Stylosanthes induced by HK-04 at room temperature. This work demonstrates an alternative to commercial antifungal agents and proposes a versatile approach to preparing environmental-friendly antifungal agents to inhibit fungal infections on crops.
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Affiliation(s)
- Zhenfei Xu
- School of Life Sciences, Hainan University, Haikou 570228, China; One Health Insititute, Hainan University, Haikou 570228, China
| | - Xiaoli Jiang
- School of Life Sciences, Hainan University, Haikou 570228, China; One Health Insititute, Hainan University, Haikou 570228, China
| | - Ye Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xiang Ma
- School of Life Sciences, Hainan University, Haikou 570228, China; One Health Insititute, Hainan University, Haikou 570228, China
| | - Yanqiong Tang
- School of Life Sciences, Hainan University, Haikou 570228, China; One Health Insititute, Hainan University, Haikou 570228, China
| | - Hong Li
- School of Life Sciences, Hainan University, Haikou 570228, China; One Health Insititute, Hainan University, Haikou 570228, China
| | - Kexian Yi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Juanjuan Li
- School of Life Sciences, Hainan University, Haikou 570228, China; One Health Insititute, Hainan University, Haikou 570228, China.
| | - Zhu Liu
- School of Life Sciences, Hainan University, Haikou 570228, China; One Health Insititute, Hainan University, Haikou 570228, China.
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Poustforoosh A, Faramarz S, Nematollahi MH, Hashemipour H, Negahdaripour M, Pardakhty A. In silico SELEX screening and statistical analysis of newly designed 5mer peptide-aptamers as Bcl-xl inhibitors using the Taguchi method. Comput Biol Med 2022; 146:105632. [PMID: 35617726 DOI: 10.1016/j.compbiomed.2022.105632] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 11/03/2022]
Abstract
Drug development for cancer treatment is a complex process that requires special efforts. Targeting crucial proteins is the most essential purpose of drug design in cancers. Bcl-xl is an anti-apoptotic protein that binds to pro-apoptotic proteins and interrupts their signals. Pro-apoptotic Bcl-xl effectors are short BH3 sequences that form an alpha helix and bind to anti-apoptotic proteins to inhibit their activity. Computational systematic evolution of ligands by exponential enrichment (SELEX) is an exclusive approach for developing peptide aptamers as potential effectors. Here, the amino acids with a high tendency for constructing an alpha-helical structure were selected. Due to the enormous number of pentapeptides, Taguchi method was used to study a selected number of peptides. The binding affinity of the peptides to Bcl-xl was assessed using molecular docking, and after analysis of the obtained results, a final set of optimized peptides was arranged and constructed. For a better comparison, three chemical compounds with approved anti-Bcl-xl activity were selected for comparison with the top-ranked 5mer peptides. The optimized peptides showed considerable binding affinity to Bcl-xl. The molecular dynamics (MD) simulation indicated that the designed peptide (PO5) could create considerable interactions with the BH3 domain of Bcl-xl. The MM/GBSA calculations revealed that these interactions were even stronger than those created by chemical compounds. In silico SELEX is a novel approach to design and evaluate peptide-aptamers. The experimental design improves the SELEX process considerably. Finally, PO5 could be considered a potential inhibitor of Bcl-xl and a potential candidate for cancer treatment.
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Affiliation(s)
- Alireza Poustforoosh
- Chemical Engineering Department, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Sanaz Faramarz
- Department of Clinical Biochemistry, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Hadi Nematollahi
- Physiology Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran; Department of Clinical Biochemistry, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hassan Hashemipour
- Chemical Engineering Department, Faculty of Engineering, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
| | - Manica Negahdaripour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Pardakhty
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
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Huang J, Wang D, Li H, Tang Y, Ma X, Tang H, Lin M, Liu Z. Antifungal activity of an artificial peptide aptamer SNP-D4 against Fusarium oxysporum. PeerJ 2022; 10:e12756. [PMID: 35223198 PMCID: PMC8877334 DOI: 10.7717/peerj.12756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/16/2021] [Indexed: 01/07/2023] Open
Abstract
Fusarium oxysporum f. sp. cubense (FOC4) is a pathogen of banana fusarium wilt, which is a serious problem that has plagued the tropical banana industry for many years. The pathogenic mechanism is complex and unclear, so the prevention and control in agricultural production applications is ineffective. SNP-D4, an artificial peptide aptamer, was identified and specifically inhibited FOC4. To evaluate the efficacy of SNP-D4, FoC4 spores were treated with purified SNP-D4 to calculate the germination and fungicide rates. Damage of FOC4 spores was observed by staining with propidium iodide (PI). Eight proteins of FOC4 were identified to have high affinity for SNP-D4 by a pull-down method combined with Q-Exactive mass spectrometry. Of these eight proteins, A0A5C6SPC6, the aldehyde dehydrogenase of FOC4, was selected as an example to scrutinize the interaction sites with SNP-D4. Molecular docking revealed that Thr66 on the peptide loop of SNP-D4 bound with Tyr437 near the catalytic center of A0A5C6SPC6. Subsequently 42 spore proteins which exhibited associations with the eight proteins were retrieved for protein-protein interaction analysis, demonstrating that SNP-D4 interfered with pathways including 'translation', 'folding, sorting and degradation', 'transcription', 'signal transduction' and 'cell growth and death', eventually causing the inhibition of growth of FOC4. This study not only investigated the possible pathogenic mechanism of FOC4, but also provided a potential antifungal agent SNP-D4 for use in the control of banana wilt disease.
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Affiliation(s)
- Junjun Huang
- College of Life Science Hainan University, Haikou, Hainan, China
| | - Dan Wang
- College of Life Science Hainan University, Haikou, Hainan, China
| | - Hong Li
- College of Life Science Hainan University, Haikou, Hainan, China
| | - Yanqiong Tang
- College of Life Science Hainan University, Haikou, Hainan, China
| | - Xiang Ma
- College of Life Science Hainan University, Haikou, Hainan, China
| | - Hongqian Tang
- College of Life Science Hainan University, Haikou, Hainan, China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhu Liu
- College of Life Science Hainan University, Haikou, Hainan, China
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Nguyen ATV, Duong BT, Park H, Yeo SJ. Development of a peptide aptamer pair-linked rapid fluorescent diagnostic system for Zika virus detection. Biosens Bioelectron 2022; 197:113768. [PMID: 34763153 DOI: 10.1016/j.bios.2021.113768] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 12/23/2022]
Abstract
A rapid diagnostic system employing an antigen detection biosensing method is needed to discriminate between Zika virus (ZIKV) and Dengue virus (DENV) due to their close antigenic homology. We developed a novel peptide pair-based flow immunochromatographic test strip (FICT) assay to detect ZIKV. Peptide aptamers, P6.1 (KQERNNWPLTWT), P29.1 (KYTTSTLKSGV), and B2.33 (KRHVWVSLSYSCAEA) were designed by paratopes and modified against the ZIKV envelope protein based on the binding affinity. An antibody-free lateral FICT was developed using a pair of peptide aptamers. In the rapid diagnostic strip, the limit of detection (LOD) for the B2.33-P6.1 peptide pair for ZIKV was 2 × 104 tissue culture infective dose TCID50/mL. Significantly, FICT could discriminate ZIKV from DENV. The stability and performance of FICT were confirmed using human sera and urine, showing a comparable LOD value. Our study demonstrated that in silico modeling could be used to develop a novel peptide pair-based FICT assay for detecting ZIKV by a rapid diagnostic test.
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Devi A, Chaitanya NSN. Designing of peptide aptamer targeting the receptor-binding domain of spike protein of SARS-CoV-2: an in silico study. Mol Divers 2021. [PMID: 33389440 DOI: 10.1007/s11030-020-10171-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022]
Abstract
Short synthetic peptide molecules which bind to a specific target protein with a high affinity to exert its function are known as peptide aptamers. The high specificity of aptamers with small-molecule targets (metal ions, dyes and theophylline; ATP) is within 1 pM and 1 μM range, whereas with the proteins (thrombin, CD4 and antibodies) it is in the nanomolar range (which is equivalent to monoclonal antibodies). The recently identified coronavirus (SARS-CoV-2) genome encodes for various proteins, such as envelope, membrane, nucleocapsid, and spike protein. Among these, the protein necessary for the virus to enter inside the host cell is spike protein. The work focuses on designing peptide aptamer targeting the spike receptor-binding domain of SARS-CoV-2. The peptide aptamer has been designed by using bacterial Thioredoxin A as the scaffold protein and an 18-residue-long peptide. The tertiary structure of the peptide aptamer is modeled and docked to spike receptor-binding domain of SARS CoV2. Molecular dynamic simulation has been done to check the stability of the aptamer and receptor-binding domain complex. It was observed that the aptamer binds to spike receptor-binding domain of SARS-CoV-2 in a similar pattern as that of ACE2. The aptamer-receptor-binding domain complex was found to be stable in a 100 ns molecular dynamic simulation. The aptamer is also predicted to be non-antigenic, non-allergenic, non-hemolytic, non-inflammatory, water-soluble with high affinity toward ACE2 than serum albumin. Thus, peptide aptamer can be a novel approach for the therapeutic treatment for SARS-CoV-2.
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Kim SH, Lee EH, Lee SC, Kim AR, Park HH, Son JW, Koh SH, Yoon MY. Development of peptide aptamers as alternatives for antibody in the detection of amyloid-beta 42 aggregates. Anal Biochem 2020; 609:113921. [PMID: 32828793 DOI: 10.1016/j.ab.2020.113921] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/13/2020] [Accepted: 08/15/2020] [Indexed: 12/14/2022]
Abstract
Alzheimer's disease (AD) causes cognitive impairment and serious social isolation. However, there are no effective treatments and even no established confirmatory diagnostic tools for the disease. Amyloid beta (Aβ) aggregation in the brain is the best-known pathognomonic mechanism of AD, so various methods for Aβ detection have been developed for the diagnosis of this disease. We synthesized two novel, ultra-sensitive peptide probes specialized in detecting Aβ aggregates, and examined their potential for future diagnostic application. The peptides are produced through phage high-throughput screening (HTS) and amplified through a serial process called biopanning, which is a repeating method of elution and amplification of probes. We picked phages specific for amyloid from two kinds of phage display. The synthesized peptides were confirmed to have excellent binding affinity to Aβ aggregates, by immunohistochemical staining and western blotting using the brains of 3X transgenic (Tg) AD mice at different stages (5-7, 12-17 months old) of AD severity. In the present study, it was confirmed that newly developed amyloid-binding peptides could be used as novel probes for the detection of Aβ aggregates, which can be used for clinical diagnosis of AD in the future.
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Affiliation(s)
- Sang-Heon Kim
- Department of Chemistry and Research Institute of Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Eun-Hye Lee
- Department of Neurology, Hanyang University College of Medicine, 11923, Gyeongchun-ro, Guri-Si, Gyeonggi-do, Republic of Korea
| | - Sang-Choon Lee
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - A-Ru Kim
- Department of Chemistry and Research Institute of Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Hyun-Hee Park
- Department of Neurology, Hanyang University College of Medicine, 11923, Gyeongchun-ro, Guri-Si, Gyeonggi-do, Republic of Korea
| | - Jeong-Woo Son
- Department of Neurology, Hanyang University College of Medicine, 11923, Gyeongchun-ro, Guri-Si, Gyeonggi-do, Republic of Korea
| | - Seong-Ho Koh
- Department of Neurology, Hanyang University College of Medicine, 11923, Gyeongchun-ro, Guri-Si, Gyeonggi-do, Republic of Korea; Department of Translational Medicine, Hanyang University Graduate School of Biomedical Science & Engineering, 11923, Gyeongchun-ro, Guri-Si, Gyeonggi-do, Republic of Korea.
| | - Moon-Young Yoon
- Department of Chemistry and Research Institute of Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
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He Y, Zhou L, Deng L, Feng Z, Cao Z, Yin Y. An electrochemical impedimetric sensing platform based on a peptide aptamer identified by high-throughput molecular docking for sensitive l-arginine detection. Bioelectrochemistry 2020; 137:107634. [PMID: 32882443 DOI: 10.1016/j.bioelechem.2020.107634] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023]
Abstract
As a primary building block for protein synthesis, l-arginine (l-Arg) is also a precursor for the synthesis of important metabolites, and is involved in various physiological and pathophysiological processes. l-Arg is a potential biomarker in clinical diagnosis and nutritional status assessment, making it valuable to quantify and monitor this biomolecule. In this study, peptide aptamers that specifically interact with l-Arg were identified by high-throughput molecular docking, and the binding capacities between the synthesized peptide aptamers and l-Arg were then measured by isothermal titration calorimetry. We hypothesized that the peptide aptamer with the greatest binding capacity could be used as the recognition element in a biosensor. A chemosynthetic peptide aptamer modified with mercaptan and spacer units (thioctic acid-GGGG-FGHIHEGY) was thus used to construct label-free electrochemical impedimetric biosensors for l-Arg based on gold electrodes. The optimum biosensor showed good sensitivity to l-Arg with a linear range of 0.1 pM-0.1 mM, and the calculated limit of detection (three times the signal-to-noise ratio) was 0.01 pM. Interference studies and assays of diluted serum samples were also carried out, and satisfactory results obtained. In conclusion, a potential method of peptide aptamer screening and biosensor fabrication for detecting small biological molecules was demonstrated.
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Affiliation(s)
- Yumin He
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Scientific Observational and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha, Hunan 410125, PR China; Animal Nutrition and Human Health Laboratory, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, PR China
| | - Li Zhou
- Collaborative Innovation Center of Micro/Nano Bio-sensing and Food Safety Inspection, Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha, Hunan 410004, PR China
| | - Lei Deng
- School of Computer Science and Engineering, Central South University, Changsha 410075, PR China
| | - Zemeng Feng
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Scientific Observational and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha, Hunan 410125, PR China.
| | - Zhong Cao
- Collaborative Innovation Center of Micro/Nano Bio-sensing and Food Safety Inspection, Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha, Hunan 410004, PR China
| | - Yulong Yin
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Scientific Observational and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha, Hunan 410125, PR China; Animal Nutrition and Human Health Laboratory, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, PR China
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Corda E, Du X, Shim SY, Klein AN, Siltberg-Liberles J, Gilch S. Interaction of Peptide Aptamers with Prion Protein Central Domain Promotes α-Cleavage of PrP C. Mol Neurobiol 2018; 55:7758-74. [PMID: 29460268 DOI: 10.1007/s12035-018-0944-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 01/31/2018] [Indexed: 11/03/2022]
Abstract
Prion diseases are infectious and fatal neurodegenerative diseases affecting humans and animals. Transmission is possible within and between species with zoonotic potential. Currently, no prophylaxis or treatment exists. Prions are composed of the misfolded isoform PrPSc of the cellular prion protein PrPC. Expression of PrPC is a prerequisite for prion infection, and conformational conversion of PrPC is induced upon its direct interaction with PrPSc. Inhibition of this interaction can abrogate prion propagation, and we have previously established peptide aptamers (PAs) binding to PrPC as new anti-prion compounds. Here, we mapped the interaction site of PA8 in PrP and modeled the complex in silico to design targeted mutations in PA8 which presumably enhance binding properties. Using these PA8 variants, we could improve PA-mediated inhibition of PrPSc replication and de novo infection of neuronal cells. Furthermore, we demonstrate that binding of PA8 and its variants increases PrPC α-cleavage and interferes with its internalization. This gives rise to high levels of the membrane-anchored PrP-C1 fragment, a transdominant negative inhibitor of prion replication. PA8 and its variants interact with PrPC at its central and most highly conserved domain, a region which is crucial for prion conversion and facilitates toxic signaling of Aβ oligomers characteristic for Alzheimer's disease. Our strategy allows for the first time to induce α-cleavage, which occurs within this central domain, independent of targeting the responsible protease. Therefore, interaction of PAs with PrPC and enhancement of α-cleavage represent mechanisms that can be beneficial for the treatment of prion and other neurodegenerative diseases.
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Inoue I, Ishikawa Y, Uraoka Y, Yamashita I, Yasueda H. Selection of a novel peptide aptamer with high affinity for TiO 2-nanoparticle through a direct electroporation with TiO 2-binding phage complexes. J Biosci Bioeng 2016; 122:528-532. [PMID: 27133793 DOI: 10.1016/j.jbiosc.2016.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/05/2016] [Accepted: 04/10/2016] [Indexed: 12/18/2022]
Abstract
We have developed an easy and rapid screening method of peptide aptamers with high affinity for a target material TiO2 using M13 phage-display and panning procedure. In a selection step, the phage-substrate complexes and Escherichia coli cells were directly applied by electric pulse for electroporation, without separating the objective phages from the TiO2 nanoparticles. Using this simple and rapid method, we obtained a novel peptide aptamer (named ST-1 with the sequence AYPQKFNNNFMS) with highly strong binding activity for TiO2. A cage-shaped protein fused with both ST-1 and an available carbon nanotube-affinity peptide was designed and produced in E. coli. The multi-functional supraprotein could efficiently mineralize a titanium-compound around the surface of single-wall carbon nanotubes (SWNTs), indicating that the ST-1 is valuable in the fabrication of nano-composite materials with titanium-compounds. The structural analysis of ST-1 variants indicated the importance of the N-terminal region (as a motif of AXPQKX6S) of the aptamer in the TiO2-binding activity.
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Affiliation(s)
- Ippei Inoue
- Frontier Research Labs., Institute for Innovation, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-8681, Japan.
| | - Yasuaki Ishikawa
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Yukiharu Uraoka
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Ichiro Yamashita
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hisashi Yasueda
- Frontier Research Labs., Institute for Innovation, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-8681, Japan
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13
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Biyani M, Kawai K, Kitamura K, Chikae M, Biyani M, Ushijima H, Tamiya E, Yoneda T, Takamura Y. PEP-on-DEP: A competitive peptide-based disposable electrochemical aptasensor for renin diagnostics. Biosens Bioelectron 2015; 84:120-5. [PMID: 26746799 DOI: 10.1016/j.bios.2015.12.078] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 12/21/2015] [Accepted: 12/22/2015] [Indexed: 11/18/2022]
Abstract
Antibody-based immunosensors are relatively less accessible to a wide variety of unreachable targets, such as low-molecular-weight biomarkers that represent a rich untapped source of disease-specific diagnostic information. Here, we present a peptide aptamer-based electrochemical sensor technology called 'PEP-on-DEP' to detect less accessible target molecules, such as renin, and to improve the quality of life. Peptide-based aptamers represent a relatively smart class of affinity binders and show great promise in biosensor development. Renin is involved in the regulation of arterial blood pressure and is an emerging biomarker protein for predicting cardiovascular risk and prognosis. To our knowledge, no studies have described aptamer molecules that can be used as new potent probes for renin. Here, we describe a portable electrochemical biosensor platform based on the newly identified peptide aptamer molecules for renin. We constructed a randomized octapeptide library pool with diversified sequences and selected renin specific peptide aptamers using cDNA display technology. We identified a few peptide aptamer sequences with a KD in the µM binding affinity range for renin. Next, we grafted the selected peptide aptamers onto gold nanoparticles and detected renin in a one-step competitive assay using our originally developed DEP (Disposable Electrochemical Printed) chip and a USB powered portable potentiostat system. We successfully detected renin in as little as 300ngmL(-1) using the PEP-on-DEP method. Thus, the generation and characterization of novel probes for unreachable target molecules by merging a newly identified peptide aptamer with electrochemical transduction allowed for the development of a more practical biosensor that, in principle, can be adapted to develop a portable, low-cost and mass-producible biosensor for point-of-care applications.
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Affiliation(s)
- Manish Biyani
- Green Devices Research Center, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan; School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan.
| | - Keiko Kawai
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Koichiro Kitamura
- JANUSYS Co. Ltd., Kamiaoki 3-12-18-508, Kawaguchi, Saitama 333-0844, Japan
| | - Miyuki Chikae
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Madhu Biyani
- BioDevice Technology Ltd., 2-13 Asahidai, Nomi, Ishikawa 923-1211, Japan
| | - Hiromi Ushijima
- BioDevice Technology Ltd., 2-13 Asahidai, Nomi, Ishikawa 923-1211, Japan
| | - Eiichi Tamiya
- BioDevice Technology Ltd., 2-13 Asahidai, Nomi, Ishikawa 923-1211, Japan; Department of Applied Physics, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takashi Yoneda
- Program Management Office for Paradigms-Establishing Centers for Fostering Medical Researchers of the Future, Kanazawa University, Takaramachi 13-1, Kanazawa, Ishikawa 920-8640, Japan
| | - Yuzuru Takamura
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
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