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Zhang H, Gao H, Liu S, Ren X, Que L, Gu X, Rong S, Ma H, Ruan J, Miao M, Qi X, Chang D, Pan H. Dual electrochemical signal "signal-on-off" sensor based on CHA-Td-HCR and CRISPR-Cas12a for MUC1 detection. Talanta 2024; 279:126665. [PMID: 39116728 DOI: 10.1016/j.talanta.2024.126665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/30/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024]
Abstract
Mucin 1 (MUC1) is frequently overexpressed in various cancers and is essential for early cancer detection. Current methods to detect MUC1 are expensive, time-consuming, and require skilled personnel. Therefore, developing a simple, sensitive, highly selective MUC1 detection sensor is necessary. In this study, we proposed a novel "signal-on-off" strategy that, in the presence of MUC1, synergistically integrates catalytic hairpin assembly (CHA) with DNA tetrahedron (Td)-based nonlinear hybridization chain reaction (HCR) to enhance the immobilization of electrochemically active methylene blue (MB) on magnetic nanoparticles (MNP), marking the MB signal "on". Concurrently, the activation of CRISPR-Cas12a by isothermal amplification products triggers the cleavage of single-stranded DNA (ssDNA) at the electrode surface, resulting in a reduction of MgAl-LDH@Fc-AuFe-MIL-101 (containing ferrocene, Fc) on the electrode, presenting the "signal-off" state. Both MB and MgAl-LDH@Fc-AuFe-MIL-101 electrochemical signals were measured and analyzed. Assay parameters were optimized, and sensitivity, stability, and linear range were assessed. Across a concentration spectrum of MUC1 spanning from 10 fg/mL to 100 ng/mL, the MB and MgAl-LDH@Fc-AuFe-MIL-101 signals were calibrated with each other, demonstrating a "signal-on-off" dual electrochemical signaling pattern. This allows for the precise and quantitative detection of MUC1 in clinical samples, offering significant potential for medical diagnosis.
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Affiliation(s)
- Hehua Zhang
- Collaborative Research Center, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; College of International Education, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Hongmin Gao
- Collaborative Research Center, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Simin Liu
- Collaborative Research Center, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Xinshui Ren
- Collaborative Research Center, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; Graduate School of Shanghai University of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Longbin Que
- Collaborative Research Center, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Xin Gu
- Collaborative Research Center, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China; School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Shengzhong Rong
- Public Health School, Mudanjiang Medical University, Mudanjiang, 157011, China
| | - Hongkun Ma
- Public Health School, Mudanjiang Medical University, Mudanjiang, 157011, China
| | - Junbin Ruan
- Faculty of Foreign Languages, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Meng Miao
- The College of Medical Technology, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Xue Qi
- School of Pharmacy, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Dong Chang
- Department of Clinical Laboratory, The Affiliated Pudong Hospital, Fudan University, Shanghai, 201399, China.
| | - Hongzhi Pan
- The Affiliated Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China.
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Vergara-Barberán M, Catalá-Icardo M, Simó-Alfonso EF, Benavente F, Herrero-Martínez JM. Aptamer-functionalized stir bar sorptive extraction for selective isolation, identification, and determination of concanavalin A in food by MALDI-TOF-MS. Mikrochim Acta 2023; 190:219. [PMID: 37178355 PMCID: PMC10182934 DOI: 10.1007/s00604-023-05795-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/10/2023] [Indexed: 05/15/2023]
Abstract
An aptamer-functionalized stir bar sorptive extraction (SBSE) coating is described for the first time devoted to selective isolation and preconcentration of an allergenic food protein, concavanalin A (Con A), followed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF-MS) determination. For this purpose, the polytetrafluoroethylene surface of commercial magnetic stir bars was properly modified and vinylized to immobilize a thiol-modified aptamer against Con A via straightforward "thiol-ene" click chemistry. The aptamer-functionalized stir bar was employed as SBSE sorbent to isolate Con A, and several parameters that can affect the extraction efficiency were investigated. Under the optimized conditions, Con A was extracted and desorbed during 30 and 45 min, respectively, at 25 °C and 600 rpm. The SBSE MALDI-TOF-MS method provided limits of detection of 0.5 μg mL-1 for Con A. Furthermore, the SBSE coating was highly selective to Con A compared to other lectins. The developed method was successfully applied to the determination of low levels of Con A in several food matrices (i.e., white beans as well as chickpea, lentils, and wheat flours). Recoveries ranged from 81 to 97% with relative standard deviations below 7%. The aptamer-based stir bars presented suitable physical and chemical long-term stability (1 month) and a reusability of 10 and 5 extraction cycles with standards and food extracts, respectively. The developed aptamer-affinity extraction devices open up the possibility of developing novel highly selective SBSE coatings for the extraction of proteins and peptides from complex samples.
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Affiliation(s)
- María Vergara-Barberán
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA•UB), University of Barcelona, C/Martí i Franquès 1-11, 08028, Barcelona, Spain
- Department of Analytical Chemistry, University of Valencia, C/Doctor Moliner 50E, 46100, Burjassot, Valencia, Spain
| | - Mónica Catalá-Icardo
- Instituto de Investigación para la Gestión Integrada de Zonas Costeras, Campus de Gandia, Universitat Politècnica de València, C/Paranimf 1, 46730, Grau de Gandia, Valencia, Spain
| | - Ernesto F Simó-Alfonso
- Department of Analytical Chemistry, University of Valencia, C/Doctor Moliner 50E, 46100, Burjassot, Valencia, Spain
| | - Fernando Benavente
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA•UB), University of Barcelona, C/Martí i Franquès 1-11, 08028, Barcelona, Spain
| | - José Manuel Herrero-Martínez
- Department of Analytical Chemistry, University of Valencia, C/Doctor Moliner 50E, 46100, Burjassot, Valencia, Spain.
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Ahirwar R. Recent advances in nanomaterials-based electrochemical immunosensors and aptasensors for HER2 assessment in breast cancer. Mikrochim Acta 2021; 188:317. [PMID: 34476602 DOI: 10.1007/s00604-021-04963-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 08/14/2021] [Indexed: 12/17/2022]
Abstract
Human epidermal growth factor receptor 2 (HER2) is one of the key molecular targets in breast cancer pathogenesis. Overexpression and/or amplification of HER2 in approximately 15-20% of breast cancer patients is associated with high mortality and poor prognosis. Accumulating evidence shows that accurate and sensitive detection of HER2 improves the survival outcomes for HER2-positive breast cancer patients from targeted therapies. The current methods of clinical determination of HER2 expression levels are based on slide-based assays that rely on invasively collected primary tumours. Alternatively, ELISA-based detection of the shredded HER2 extracellular domain (HER2-ECD) of has been suggested as a surrogate method for monitoring disease progress and treatment response in breast cancer patients. In the past decade, biosensors have emerged as an alternative modality for the detection of circulating HER2-ECD in human serum samples. In particular, electrochemical biosensors based on nanomaterials and antibodies and aptamers have been increasingly developed as promising tools for rapid, sensitive, and cost-effective detection of HER2-ECD. These biosensors harness the high affinity and specificity of antibodies and aptamers, and unique conductive properties, biocompatibility, large surface area, and chemical stability of nanomaterials for selective and sensitive assessment of the HER2. This review provides an overview of the recent advances in the application of nanomaterials-based immunosensors and aptasensors for detection of circulating HER2-ECD. In particular, various electrochemical techniques, detection approaches, and nanomaterials are discussed. Further, analytical figures of merit of various HER2 immunosensors and aptasensors are compared. Finally, possible challenges and potential opportunities for biosensor-based detection of HER2-ECD are discussed.
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Affiliation(s)
- Rajesh Ahirwar
- Department of Environmental Biochemistry, ICMR- National Institute for Research in Environmental Health, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, 462030, India.
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Ahirwar R, Khan N, Kumar S. Aptamer-based sensing of breast cancer biomarkers: a comprehensive review of analytical figures of merit. Expert Rev Mol Diagn 2021; 21:703-721. [PMID: 33877005 DOI: 10.1080/14737159.2021.1920397] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Accurate determination of the aberrantly expressed biomarkers such as human epidermal growth factor receptor 2 (HER2), carcinoembryonic antigen (CEA), platelet-derived growth factor (PDGF), mucin 1 (MUC1), and vascular endothelial growth factor VEGF165 have played an essential role in the clinical management of the breast cancer. Assessment of these cancer-specific biomarkers has conventionally relied on time-taking methods like the enzyme-linked immunosorbent assay and immunohistochemistry. However, recent development in the aptamer-based diagnostics has allowed developing tools that may substitute the conventional means of biomarker assessment in breast cancer. Adopting the aptamer-based diagnostic tools (aptasensors) to clinical practices will depend on their analytical performance on clinical samples. AREAS COVERED In this review, we provide an overview of the analytical merits of HER2, CEA, PDGF, MUC1, and VEGF165 aptasensors. Scopus and Pubmed databases were searched for studies reporting aptasensor development for the listed breast cancer biomarkers in the past one decade. Linearity, detection limit, and response time are emphasized. EXPERT OPINION In our opinion, aptasensors have proven to be on a par with the antibody-based methods for detection of various breast cancer biomarkers. Though robust validation of the aptasensors on significant sample size is required, their ability to detect pathophysiological range of biomarkers suggest the possibility of future clinical adoption.
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Affiliation(s)
- Rajesh Ahirwar
- Department of Environmental Biochemistry, ICMR- National Institute for Research in Environmental Health, Bhopal, India
| | - Nabab Khan
- Department of Environmental Biochemistry, ICMR- National Institute for Research in Environmental Health, Bhopal, India
| | - Saroj Kumar
- School of Biosciences, Apeejay Stya University, Gurgaon, India
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Allemailem KS, Almatroudi A, Alsahli MA, Basfar GT, Alrumaihi F, Rahmani AH, Khan AA. Recent advances in understanding oligonucleotide aptamers and their applications as therapeutic agents. 3 Biotech 2020; 10:551. [PMID: 33269185 PMCID: PMC7686427 DOI: 10.1007/s13205-020-02546-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022] Open
Abstract
The innovative discovery of aptamers was based on target-specific treatment in clinical diagnostics and therapeutics. Aptamers are synthetic, single-stranded oligonucleotides, simply described as chemical antibodies, which can bind to diverse targets with high specificity and affinity. Aptamers are synthesized by the SELEX technique, and possess distinctive properties as small size (10-50 kDa), higher stability, easy manufacture and less immunogenicity. These oligonucleotides are easily degraded by nucleases, so require some important modifications like capping and incorporation of modified nucleotides. RNA aptamers can be modified chemically on 2' positions using -NH3, -F, -deoxy, or -OMe groups to enhance their nuclease resistance. Aptamers have been employed for multiple purposes, as direct drugs or aptamer-drug conjugates targeted against different diseased cells. Different aptamer-conjugated nanovehicles (e.g., micelles, liposomes, silica nano-shells) have been designed to transport diverse anticancer-drugs like doxorubicin and cisplatin in bulk to minimize systemic cytotoxicity. Some drug-loaded nanovehicles (up to 97% loading capacity) and conjugated with specific aptamer resulted in more than 60% tumor inhibition as compared to unconjugated drug-loaded nanovehicles which showed only 31% cancer inhibition. In addition, aptamers have been widely used in basic research, food safety, environmental monitoring, clinical diagnostics and therapeutics. Different FDA-approved RNA and DNA aptamers are now available in the market, used for the treatment of diverse diseases, especially cancer. These aptamers include Macugen, Pegaptanib, etc. Despite a good progress in aptamer use, the present-day chemotherapeutics and drug targeting systems still face great challenges. Here in this review article, we are discussing nucleic acid aptamers, preparation, role in the transportation of different nanoparticle vehicles and their applications as therapeutic agents.
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Affiliation(s)
- Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
- Department of Basic Health Sciences, College of Applied Medical Sciences, Qassim University, P.O. Box 6699, Buraydah, 51452 Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Mohammed A. Alsahli
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Ghaiyda Talal Basfar
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Amjad Ali Khan
- Department of Basic Health Sciences, College of Applied Medical Sciences, Qassim University, P.O. Box 6699, Buraydah, 51452 Saudi Arabia
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Rodriguez EL, Poddar S, Iftekhar S, Suh K, Woolfork AG, Ovbude S, Pekarek A, Walters M, Lott S, Hage DS. Affinity chromatography: A review of trends and developments over the past 50 years. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1157:122332. [PMID: 32871378 PMCID: PMC7584770 DOI: 10.1016/j.jchromb.2020.122332] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 12/16/2022]
Abstract
The field of affinity chromatography, which employs a biologically-related agent as the stationary phase, has seen significant growth since the modern era of this method began in 1968. This review examines the major developments and trends that have occurred in this technique over the past five decades. The basic principles and history of this area are first discussed. This is followed by an overview of the various supports, immobilization strategies, and types of binding agents that have been used in this field. The general types of applications and fields of use that have appeared for affinity chromatography are also considered. A survey of the literature is used to identify major trends in these topics and important areas of use for affinity chromatography in the separation, analysis, or characterization of chemicals and biochemicals.
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Affiliation(s)
| | - Saumen Poddar
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Sazia Iftekhar
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Kyungah Suh
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Ashley G Woolfork
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Susan Ovbude
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Allegra Pekarek
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Morgan Walters
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Shae Lott
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA.
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7
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Mahmoudi Gomari M, Saraygord-Afshari N, Farsimadan M, Rostami N, Aghamiri S, Farajollahi MM. Opportunities and challenges of the tag-assisted protein purification techniques: Applications in the pharmaceutical industry. Biotechnol Adv 2020; 45:107653. [PMID: 33157154 DOI: 10.1016/j.biotechadv.2020.107653] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 01/16/2023]
Abstract
Tag-assisted protein purification is a method of choice for both academic researches and large-scale industrial demands. Application of the purification tags in the protein production process can help to save time and cost, but the design and application of tagged fusion proteins are challenging. An appropriate tagging strategy must provide sufficient expression yield and high purity for the final protein products while preserving their native structure and function. Thanks to the recent advances in the bioinformatics and emergence of high-throughput techniques (e.g. SEREX), many new tags are introduced to the market. A variety of interfering and non-interfering tags have currently broadened their application scope beyond the traditional use as a simple purification tool. They can take part in many biochemical and analytical features and act as solubility and protein expression enhancers, probe tracker for online visualization, detectors of post-translational modifications, and carrier-driven tags. Given the variability and growing number of the purification tags, here we reviewed the protein- and peptide-structured purification tags used in the affinity, ion-exchange, reverse phase, and immobilized metal ion affinity chromatographies. We highlighted the demand for purification tags in the pharmaceutical industry and discussed the impact of self-cleavable tags, aggregating tags, and nanotechnology on both the column-based and column-free purification techniques.
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Affiliation(s)
- Mohammad Mahmoudi Gomari
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Neda Saraygord-Afshari
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran.
| | - Marziye Farsimadan
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - Neda Rostami
- Department of Chemical Engineering, Faculty of Engineering, Arak University, Iran
| | - Shahin Aghamiri
- Student research committee, Department of medical biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad M Farajollahi
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
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8
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Perret G, Boschetti E. Aptamer-Based Affinity Chromatography for Protein Extraction and Purification. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 174:93-139. [PMID: 31485702 DOI: 10.1007/10_2019_106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aptamers are oligonucleotide molecules able to recognize very specifically proteins. Among the possible applications, aptamers have been used for affinity chromatography with effective results and advantages over most advanced protein separation technologies. This chapter first discusses the context of the affinity chromatography with aptamer ligands. With the adaptation of SELEX, the chemical modifications of aptamers to comply with the covalent coupling and the separation process are then extensively presented. A focus is then made about the most important applications for protein separation with real-life examples and the comparison with immunoaffinity chromatography. In spite of well-advanced demonstrations and the extraordinary potential developments, a significant optimization work is still due to deserve large-scale applications with all necessary validations. Graphical Abstract Aptamer-protein complexes by X-ray crystallography.
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9
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Matos MJB, Pina AS, Roque ACA. Rational design of affinity ligands for bioseparation. J Chromatogr A 2020; 1619:460871. [PMID: 32044126 DOI: 10.1016/j.chroma.2020.460871] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/05/2020] [Accepted: 01/08/2020] [Indexed: 11/25/2022]
Abstract
Affinity adsorbents have been the cornerstone in protein purification. The selective nature of the molecular recognition interactions established between an affinity ligands and its target provide the basis for efficient capture and isolation of proteins. The plethora of affinity adsorbents available in the market reflects the importance of affinity chromatography in the bioseparation industry. Ligand discovery relies on the implementation of rational design techniques, which provides the foundation for the engineering of novel affinity ligands. The main goal for the design of affinity ligands is to discover or improve functionality, such as increased stability or selectivity. However, the methodologies must adapt to the current needs, namely to the number and diversity of biologicals being developed, and the availability of new tools for big data analysis and artificial intelligence. In this review, we offer an overview on the development of affinity ligands for bioseparation, including the evolution of rational design techniques, dating back to the years of early discovery up to the current and future trends in the field.
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Affiliation(s)
- Manuel J B Matos
- UCIBIO, Chemistry Department, School of Sciences and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Ana S Pina
- UCIBIO, Chemistry Department, School of Sciences and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - A C A Roque
- UCIBIO, Chemistry Department, School of Sciences and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal.
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10
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Zhang Q, Yang Y, Zhi Y, Wang X, Wu Y, Zheng Y. Aptamer-modified magnetic metal-organic framework MIL-101 for highly efficient and selective enrichment of ochratoxin A. J Sep Sci 2018; 42:716-724. [PMID: 30548208 DOI: 10.1002/jssc.201800840] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 11/03/2018] [Accepted: 11/16/2018] [Indexed: 12/17/2022]
Abstract
A facile and efficient strategy is developed to modify aptamers on the surface of the magnetic metal-organic framework MIL-101 for the rapid magnetic solid-phase extraction of ochratoxin A. To the best of our knowledge, this is the first attempt to create a robust aptamer-modified magnetic MIL-101 with covalent bonding for the magnetic separation and enrichment of ochratoxin A. The saturated adsorption of ochratoxin A by aptamer-modified magnetic MIL-101 was 7.9 times greater than that by magnetic metal-organic framework MIL-101 due to the former's high selective recognition as well as good stability. It could be used for extraction more than 12 times with no significant changes in the extraction efficiency. An aptamer-modified magnetic MIL-101-based method of magnetic solid-phase extraction combined with ultra high performance liquid chromatography with tandem mass spectrometry was developed for the determination of trace ochratoxin A with limit of detection of 0.067 ng/L. Ochratoxin A of 4.53-13.7 ng/kg was determined in corn and peanut samples. The recoveries were in the range 82.8-108% with a relative standard deviation (n = 5) of 4.5-6.5%. These results show that aptamer-modified magnetic MIL-101 exhibits selective and effective enrichment performance and have excellent potential for the analysis of ultra-trace targets from complex matrices.
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Affiliation(s)
- Qianchun Zhang
- Key Laboratory of Chemical Synthesis and Environmental Pollution Control-Remediation Technology of Guizhou Province, School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi, P. R. China
| | - Yanqun Yang
- Key Laboratory of Chemical Synthesis and Environmental Pollution Control-Remediation Technology of Guizhou Province, School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi, P. R. China
| | - Yongzhi Zhi
- Key Laboratory of Chemical Synthesis and Environmental Pollution Control-Remediation Technology of Guizhou Province, School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi, P. R. China
| | - Xingyi Wang
- Key Laboratory of Chemical Synthesis and Environmental Pollution Control-Remediation Technology of Guizhou Province, School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi, P. R. China
| | - Yun Wu
- Key Laboratory of Chemical Synthesis and Environmental Pollution Control-Remediation Technology of Guizhou Province, School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi, P. R. China
| | - Yuguo Zheng
- Key Laboratory of Chemical Synthesis and Environmental Pollution Control-Remediation Technology of Guizhou Province, School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi, P. R. China
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11
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Kim AR, Ha NR, Jung IP, Kim SH, Yoon MY. Development of a ssDNA aptamer system with reduced graphene oxide (rGO) to detect nonylphenol ethoxylate in domestic detergent. J Mol Recognit 2018; 32:e2764. [PMID: 30251354 DOI: 10.1002/jmr.2764] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 07/10/2018] [Accepted: 08/20/2018] [Indexed: 12/27/2022]
Abstract
Endocrine-disrupting chemicals are a major public health problem throughout the world. In the human body, these compounds functionalize the same as sexual hormones, inducing precocious puberty, gynecomastia, etc. To help prevent this occurrence, a simple detection system is needed. In this study, a nonylphenol ethoxylate (NPE)-specific aptamer was selected by reduced graphene oxide-systematic evolution of ligands by exponential enrichment. A random ssDNA library was incubated with rGO for adsorption, followed by elution with the target molecule. As a result of screening, a DNA aptamer was found that specifically bounds to the target with high binding affinity (Kd = 100.9 ± 13.2 nM) and had a low limit of detection (LOD = 696 pM). Furthermore, this NPE-binding aptamer bounds selectively to the target. Characterization of the aptamer was confirmed by measuring the fluorescence signal recovery from rGO. In addition, detection of NPE was performed with several water samples, and the detection accuracy was 100 ± 10%. From these results, we expect that this aptamer could be applied to an on-site detection system for NPE in industrial sites or domestic fields.
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Affiliation(s)
- A-Ru Kim
- Department of Chemistry and Research Institute of Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Na-Reum Ha
- Department of Chemistry and Research Institute of Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - In-Pil Jung
- Department of Chemistry and Research Institute of Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Sang-Heon Kim
- Department of Chemistry and Research Institute of Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Moon-Young Yoon
- Department of Chemistry and Research Institute of Natural Sciences, Hanyang University, Seoul, Republic of Korea
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12
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Khodadadi M, Malekpour A, Mehrgardi MA. Aptamer functionalized magnetic nanoparticles for effective extraction of ultratrace amounts of aflatoxin M1 prior its determination by HPLC. J Chromatogr A 2018; 1564:85-93. [DOI: 10.1016/j.chroma.2018.06.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 04/03/2018] [Accepted: 06/08/2018] [Indexed: 12/11/2022]
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13
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Aptamer-based polyhedral oligomeric silsesquioxane (POSS)-containing hybrid affinity monolith prepared via a "one-pot" process for selective extraction of ochratoxin A. J Chromatogr A 2018; 1563:37-46. [PMID: 29866505 DOI: 10.1016/j.chroma.2018.05.044] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 05/17/2018] [Accepted: 05/22/2018] [Indexed: 11/24/2022]
Abstract
A novel aptamer-based polyhedral oligomeric silsesquioxane (POSS)-containing hybrid affinity monolith has been prepared with a facile "one-pot" process simultaneously via "free radical polymerization" and "thiol-ene" click reaction, and used for on-line selective extraction and practical analysis to trace ochratoxin A (OTA). By using the ternary porogenic mixture composed of water/DMF/PEG, a homogeneous polymerization mixture with POSS chemicals, acrylate-based monomers and aptamer aqueous solution was obtained, and the copolymerization of POSS chemicals, polymer monomers and aptamer aqueous solution was systematically studied. Characterizations such as the morphology, FT-IR and fluorescence spectra, mechanical stability, dynamic binding capacity, cross-reactivity and selectivity of the resultant affinity monolith were also evaluated. Attributed to the porous monolithic structure and aptamer-based affinity interaction, acceptable selective recognition and recovery yields towards trace OTA were obtained. With a 5-fold volume enrichment, the limit of detection (LOD) and limit of quantitation (LOQ) of OTA in fortified beer samples were gained at 0.025 ng/mL (S/N = 3) and 0.045 ng/mL (S/N = 10), respectively. It could be competent for the sensitive measure of actual OTA residues in real beer samples. In comparison with the previously reported strategies containing common "sol-gel" chemistry, the proposed protocol to fabricating aptamer-modified POSS-containing hybrid affinity monolith showed a simpler preparation with acceptable selectivity and higher recovery to trace OTA.
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Beloborodov SS, Bao J, Krylova SM, Shala-Lawrence A, Johnson PE, Krylov SN. Aptamer facilitated purification of functional proteins. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1073:201-206. [PMID: 29287247 DOI: 10.1016/j.jchromb.2017.12.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/15/2017] [Accepted: 12/15/2017] [Indexed: 12/13/2022]
Abstract
DNA aptamers are attractive capture probes for affinity chromatography since, in contrast to antibodies, they can be chemically synthesized and, in contrast to tag-specific capture probes (such as Nickel-NTA or Glutathione), they can be used for purification of proteins free of genetic modifications (such as His or GST tags). Despite these attractive features of aptamers as capture probes, there are only a few reports on aptamer-based protein purification and none of them includes a test of the purified protein's activity, thus, leaving discouraging doubts about method's ability to purify proteins in their active state. The goal of this work was to prove that aptamers could facilitate isolation of active proteins. We refined a complete aptamer-based affinity purification procedure, which takes 4 h to complete. We further applied this procedure to purify two recombinant proteins, MutS and AlkB, from bacterial cell culture: 0.21 mg of 85%-pure AlkB from 4 mL of culture and 0.24 mg of 82%-pure MutS from 0.5 mL of culture. Finally, we proved protein activity by two capillary electrophoresis based assays: an enzymatic assay for AlkB and a DNA-binding assay for MutS. We suggest that in combination with aptamer selection for non-purified protein targets in crude cell lysate, aptamer-based purification provides a means of fast isolation of tag-free recombinant proteins in their native state without the use of antibodies.
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Affiliation(s)
- Stanislav S Beloborodov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Jiayin Bao
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Svetlana M Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Agnesa Shala-Lawrence
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Philip E Johnson
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sergey N Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada.
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Perret G, Boschetti E. Aptamer affinity ligands in protein chromatography. Biochimie 2017; 145:98-112. [PMID: 29054800 DOI: 10.1016/j.biochi.2017.10.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 10/12/2017] [Indexed: 02/07/2023]
Abstract
The present review deals with the place of single chain oligonucleotide ligands (aptamers) in affinity chromatography applied to proteins. Aptamers are not the only affinity ligands available but they represent an emerging and highly promising route that advantageously competes with antibodies in immunopurification processes. A historical background of affinity chromatography from the beginning of the discipline to the most recent outcomes is first presented. Then the focus is centered on aptamers which represent the last step so far to the long quest for affinity ligands associating very high specificity, availability and strong stability against most harsh cleaning agents required in chromatography. Then technologies of ligand selection from large libraries followed by the most appropriate chemical grafting approaches are described and supported by a number of bibliographic references. Experimental results assembled from relevant published paper are reported; they are selected by their practical applicability and potential use at large scale. The review concludes with specific remarks and future developments that are expected in the near future to turn this technology into a large acceptance for preparative applications.
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Forier C, Boschetti E, Ouhammouch M, Cibiel A, Ducongé F, Nogré M, Tellier M, Bataille D, Bihoreau N, Santambien P, Chtourou S, Perret G. DNA aptamer affinity ligands for highly selective purification of human plasma-related proteins from multiple sources. J Chromatogr A 2017; 1489:39-50. [PMID: 28179082 DOI: 10.1016/j.chroma.2017.01.031] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/04/2017] [Accepted: 01/06/2017] [Indexed: 01/18/2023]
Abstract
Nucleic acid aptamers are promising ligands for analytical and preparative-scale affinity chromatography applications. However, a full industrial exploitation requires that aptamer-grafted chromatography media provide a number of high technical standards that remained largely untested. Ideally, they should exhibit relatively high binding capacity associated to a very high degree of specificity. In addition, they must be highly resistant to harsh cleaning/sanitization conditions, as well as to prolonged and repeated exposure to biological environment. Here, we present practical examples of aptamer affinity chromatography for the purification of three human therapeutic proteins from various sources: Factor VII, Factor H and Factor IX. In a single chromatographic step, three DNA aptamer ligands enabled the efficient purification of their target protein, with an unprecedented degree of selectivity (from 0.5% to 98% of purity in one step). Furthermore, these aptamers demonstrated a high stability under harsh sanitization conditions (100h soaking in 1M NaOH). These results pave the way toward a wider adoption of aptamer-based affinity ligands in the industrial-scale purification of not only plasma-derived proteins but also of any other protein in general.
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Affiliation(s)
| | | | | | | | - Frédéric Ducongé
- CEA, I2BM, MIRCen, UMR 9199, Université Paris Saclay, Fontenay aux Roses, France
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Citartan M, Ch'ng ES, Rozhdestvensky TS, Tang TH. Aptamers as the ‘capturing’ agents in aptamer-based capture assays. Microchem J 2016. [DOI: 10.1016/j.microc.2016.04.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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18
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Ahirwar R, Vellarikkal SK, Sett A, Sivasubbu S, Scaria V, Bora U, Borthakur BB, Kataki AC, Sharma JD, Nahar P. Aptamer-Assisted Detection of the Altered Expression of Estrogen Receptor Alpha in Human Breast Cancer. PLoS One 2016; 11:e0153001. [PMID: 27043307 PMCID: PMC4820125 DOI: 10.1371/journal.pone.0153001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 03/22/2016] [Indexed: 12/21/2022] Open
Abstract
An increase in the expression of estrogen receptors (ER) and the expanded population of ER-positive cells are two common phenotypes of breast cancer. Detection of the aberrantly expressed ERα in breast cancer is carried out using ERα-antibodies and radiolabelled ligands to make decisions about cancer treatment and targeted therapy. Capitalizing on the beneficial advantages of aptamer over the conventional antibody or radiolabelled ligand, we have identified a DNA aptamer that selectively binds and facilitates the detection of ERα in human breast cancer tissue sections. The aptamer is identified using the high throughput sequencing assisted SELEX screening. Biophysical characterization confirms the binding and formation of a thermodynamically stable complex between the identified DNA aptamer (ERaptD4) and ERα (Ka = 1.55±0.298×108 M-1; ΔH = 4.32×104±801.1 cal/mol; ΔS = -108 cal/mol/deg). Interestingly, the specificity measurements suggest that the ERaptD4 internalizes into ERα-positive breast cancer cells in a target-selective manner and localizes specifically in the nuclear region. To harness these characteristics of ERaptD4 for detection of ERα expression in breast cancer samples, we performed the aptamer-assisted histochemical analysis of ERα in tissue samples from breast cancer patients. The results were validated by performing the immunohistochemistry on same samples with an ERα-antibody. We found that the two methods agree strongly in assay output (kappa value = 0.930, p-value <0.05 for strong ERα positive and the ERα negative samples; kappa value = 0.823, p-value <0.05 for the weak/moderate ER+ve samples, n = 20). Further, the aptamer stain the ERα-positive cells in breast tissues without cross-reacting to ERα-deficient fibroblasts, adipocytes, or the inflammatory cells. Our results demonstrate a significant consistency in the aptamer-assisted detection of ERα in strong ERα positive, moderate ERα positive and ERα negative breast cancer tissues. We anticipate that the ERaptD4 aptamer targeting ERα may potentially be used for an efficient grading of ERα expression in cancer tissues.
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Affiliation(s)
- Rajesh Ahirwar
- Department of System and Chemical Biology, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative research, CSIR- Institute of Genomics and Integrative Biology, Delhi, India
| | - Shamsudheen Karuthedath Vellarikkal
- Department of System and Chemical Biology, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative research, CSIR- Institute of Genomics and Integrative Biology, Delhi, India
| | - Arghya Sett
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, India
| | - Sridhar Sivasubbu
- Department of System and Chemical Biology, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative research, CSIR- Institute of Genomics and Integrative Biology, Delhi, India
| | - Vinod Scaria
- Department of System and Chemical Biology, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative research, CSIR- Institute of Genomics and Integrative Biology, Delhi, India
| | - Utpal Bora
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, India
| | | | | | | | - Pradip Nahar
- Department of System and Chemical Biology, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative research, CSIR- Institute of Genomics and Integrative Biology, Delhi, India
- * E-mail:
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Adsorption and separation of HCV particles by novel affinity aptamer-functionalized adsorbents. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1017-1018:174-181. [DOI: 10.1016/j.jchromb.2016.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/16/2016] [Accepted: 03/03/2016] [Indexed: 01/11/2023]
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Matsuda R, Rodriguez E, Suresh D, Hage DS. Chromatographic immunoassays: strategies and recent developments in the analysis of drugs and biological agents. Bioanalysis 2015; 7:2947-66. [PMID: 26571109 PMCID: PMC4820777 DOI: 10.4155/bio.15.206] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A chromatographic immunoassay is a technique in which an antibody or antibody-related agent is used as part of a chromatographic system for the isolation or measurement of a specific target. Various binding agents, detection methods, supports and assay formats have been developed for this group of methods, and applications have been reported that range from drugs, hormones and herbicides to peptides, proteins and bacteria. This review discusses the general principles and applications of chromatographic immunoassays, with an emphasis being given to methods and formats that have been developed for the analysis of drugs and biological agents. The relative advantages or limitations of each format are discussed. Recent developments and research in this field, as well as possible future directions, are also considered.
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Affiliation(s)
- Ryan Matsuda
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, USA
| | - Elliott Rodriguez
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, USA
| | - Doddavenkatanna Suresh
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, USA
- Home Department: Department of Chemistry, Tumkur University, Tumkur, Karnataka 572103, India
| | - David S Hage
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, USA
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Oktay K, Köse LP, Şendil K, Gültekin MS, Gülçin İ, Supuran CT. The synthesis of (Z)-4-oxo-4-(arylamino)but-2-enoic acids derivatives and determination of their inhibition properties against human carbonic anhydrase I and II isoenzymes. J Enzyme Inhib Med Chem 2015; 31:939-45. [PMID: 26308288 DOI: 10.3109/14756366.2015.1071808] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The synthesis of (Z)-4-oxo-4-(arylamino)but-2-enoic acid (4) derivatives containing structural characteristics that can be used for the synthesis of several active molecules, is presented. Some of the butenoic acid derivatives (4a, 4c, 4e, 4i, 4j, 4k) are synthesized following literature procedures and at the end of the reaction. In addition, structures of all synthesized derivatives (4a-4m) were determined by (1)H-NMR, (13)C-NMR and IR spectroscopy. Carbonic anhydrase is a metalloenzyme involved in many crucial physiologic processes as it catalyzes a simple but fundamental reaction, the reversible hydration of carbon dioxide to bicarbonate and protons. Significant results were obtained by evaluating the enzyme inhibitory activities of these derivatives against human carbonic anhydrase hCA I and II isoenzymes (hCA I and II). Butenoic acid derivatives (4a-4m) strongly inhibited hCA I and II with Kis in the low nanomolar range of 1.85 ± 0.58 to 5.04 ± 1.46 nM against hCA I and in the range of 2.01 ± 0.52 to 2.94 ± 1.31 nM against hCA II.
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Affiliation(s)
- Koray Oktay
- a Faculty of Science, Department of Chemistry , Ataturk University , Erzurum , Turkey
| | - Leyla Polat Köse
- a Faculty of Science, Department of Chemistry , Ataturk University , Erzurum , Turkey
| | - Kıvılcım Şendil
- b Faculty of Science and Arts, Department of Chemistry , Kafkas University , Kars , Turkey
| | | | - İlhami Gülçin
- a Faculty of Science, Department of Chemistry , Ataturk University , Erzurum , Turkey .,c Department of Zoology , College of Science, King Saud University , Riyadh , Saudi Arabia
| | - Claudiu T Supuran
- d Dipartimento di Chimica Ugo Schiff, Università degli Studi di Firenze , Sesto Fiorentino (Firenze) , Italy , and.,e Neurofarba Department, Section of Pharmaceutical and Nutriceutical Sciences, Università degli Studi di Firenze , Sesto Fiorentino (Florence) , Italy
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