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Liang G, Zhao J, Gao Y, Xie T, Zhen J, Pan L, Gong W. Application and evaluation of molecular docking for aptamer and small molecular interaction - A case study with tetracycline antibiotics. Talanta 2024; 266:124942. [PMID: 37459789 DOI: 10.1016/j.talanta.2023.124942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/28/2023] [Accepted: 07/12/2023] [Indexed: 09/20/2023]
Abstract
Molecular docking (MD) analysis is currently the most commonly used theoretical simulation method to investigate the interaction of aptamers (receptors) and small molecules (ligands) and understand the recognition mechanism between them at a molecular level. Using the specific aptamers of tetracycline antibiotics (tetracycline (TET), oxytetracycline (OTC), doxycycline (DOC)) as the docking models, three steady-state aptamers of tertiary structures (SATS) were established for each aptamer with the UNAFold and RNAComposer tools. The binding free energy (BFE), docking score (DS), and binding site (base) of the specific ligands (TET, OTC, and DOC) with their respective SATS were obtained by molecular docking. The results revealed one or more binding sites in the established SATS of the aptamers. The BFE and DS of different binding sites of one specific SATS varied significantly. The results also revealed that the site with the highest BFE represented the most dominant binding site, even if it was not the SATS with minimum energy. The BFE values could also be used to evaluate the affinity and specificity of the aptamer to its target. For the first time, this study proposes a method for MD analysis of the aptamer and its target based on different SATS, clarification of the binding mode, and prediction of the binding sites (bases). This study provides a theoretical basis for tailoring; structural optimization; and base modification of aptamers; identifying aptamers with high affinity and specificity.
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Affiliation(s)
- Gang Liang
- Institute of Quality Standard and Testing Technology, BAAFS (Beijing Academy of Agriculture and Forestry Sciences), Beijing, 100097, China; Risk Assessment Lab for Agro-products (Beijing), Ministry of Agriculture, Beijing, 100097, China.
| | - Jie Zhao
- Institute of Quality Standard and Testing Technology, BAAFS (Beijing Academy of Agriculture and Forestry Sciences), Beijing, 100097, China; Risk Assessment Lab for Agro-products (Beijing), Ministry of Agriculture, Beijing, 100097, China
| | - Yufei Gao
- College of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang, 050024, China
| | - Tao Xie
- Chengdu University, 610000, Chengdu, China
| | - Jianhui Zhen
- Shijiazhuang Customs Technology Center PR China, Shijiazhuang, 050051, China.
| | - Ligang Pan
- Institute of Quality Standard and Testing Technology, BAAFS (Beijing Academy of Agriculture and Forestry Sciences), Beijing, 100097, China; Risk Assessment Lab for Agro-products (Beijing), Ministry of Agriculture, Beijing, 100097, China
| | - Wenwen Gong
- Institute of Quality Standard and Testing Technology, BAAFS (Beijing Academy of Agriculture and Forestry Sciences), Beijing, 100097, China; Risk Assessment Lab for Agro-products (Beijing), Ministry of Agriculture, Beijing, 100097, China.
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Algethami FK, Rabti A, Mastouri M, Ben Aoun S, Abdulkhair BY, Raouafi N. In silico selection of an aptamer for the design of aptamer-modified magnetic beads bearing ferrocene co-immobilized label for capacitive detection of acetamiprid. Talanta 2023; 258:124445. [PMID: 36924636 DOI: 10.1016/j.talanta.2023.124445] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/04/2023] [Accepted: 03/09/2023] [Indexed: 03/12/2023]
Abstract
In silico evaluation of aptamer/target interactions can facilitate the development of efficient biosensor with high specificity and affinity. In this work, we present in silico, i.e. structural similarity, molecular docking and molecular dynamics selection of the aptamer with sufficient binding properties for acetamiprid (ACE), a nicotine-like pesticide, and its use to design aptamer-modified magnetic beads bearing ferrocene co-immobilized label for capacitive detection of ACE. Taking advantages of the aptamer higher stability and binding affinity, the specific properties of magnetic beads and the redox properties of ferrocene moiety, the developed aptasensor showed promising analytical performances for ACE detection, using electrochemical capacitance spectroscopy, with a linear response ranging from 1 fM to 100 pM and a limit of detection of 0.94 fM (S/N = 3). Furthermore, it was successfully applied to detect ACE in fortified tomatoes samples, proving a promising approach for routine detection of pesticide in real agricultural samples.
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Affiliation(s)
- Faisal K Algethami
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, P.O. Box 90950, Riyadh, 11623, Saudi Arabia.
| | - Amal Rabti
- Sensors and Biosensors Group, Analytical Chemistry and Electrochemistry Lab (LR99ES15), University of Tunis El Manar, Tunis El Manar, 2092, Tunis, Tunisia
| | - Mohamed Mastouri
- Sensors and Biosensors Group, Analytical Chemistry and Electrochemistry Lab (LR99ES15), University of Tunis El Manar, Tunis El Manar, 2092, Tunis, Tunisia
| | - Sami Ben Aoun
- Department of Chemistry, Faculty of Science, Taibah University, P.O Box 30002, Al-Madinah Al-Munawwarah, Saudi Arabia
| | - Babiker Y Abdulkhair
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University, P.O. Box 90950, Riyadh, 11623, Saudi Arabia
| | - Noureddine Raouafi
- Sensors and Biosensors Group, Analytical Chemistry and Electrochemistry Lab (LR99ES15), University of Tunis El Manar, Tunis El Manar, 2092, Tunis, Tunisia.
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Li T, Wang J, Zhu L, Li C, Chang Q, Xu W. Advanced screening and tailoring strategies of pesticide aptamer for constructing biosensor. Crit Rev Food Sci Nutr 2022; 63:10974-10994. [PMID: 35699641 DOI: 10.1080/10408398.2022.2086210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The rapid development of aptamers has helped address the challenges presented by the wide existed pesticides contaminations. Screening of aptamers with excellent performance is a prerequisite for successfully constructing biosensors, while further tailoring of aptamers with enhanced activity greatly improved the assay performance. Firstly, this paper reviewed the advanced screening strategies for pesticides aptamers, including immobilization screening that preserves the native structures of targets, non-immobilized screening based on nanomaterials, capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX), virtual screening in silico, high-throughput selection, and rational secondary library generation methods, which contributed significantly to improve the success rate of screening, reduce the screening time, and ensure aptamer binding affinity. Secondly, the precise tailoring strategies for pesticides aptamers were modularly elaborated, containing deletion, splitting, elongation, and fusion, which provided various advantages like cost-efficiency, enhanced binding affinity, and new derived functional motifs. Thirdly, the developed aptamer-based biosensors (aptasensors) for pesticide detection were systematically reviewed according to the different signal output modes. Finally, the challenges and future perspectives of pesticide detection are discussed comprehensively.
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Affiliation(s)
- Tianshun Li
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University,, Beijing, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Jia Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University,, Beijing, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University,, Beijing, China
| | - Chenwei Li
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University,, Beijing, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Qiaoying Chang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University,, Beijing, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University,, Beijing, China
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4
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Biosensors and biopolymer-based nanocomposites for smart food packaging: Challenges and opportunities. Food Packag Shelf Life 2021. [DOI: 10.1016/j.fpsl.2021.100745] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Adebayo EA, Azeez MA, Alao MB, Oke AM, Aina DA. Fungi as veritable tool in current advances in nanobiotechnology. Heliyon 2021; 7:e08480. [PMID: 34901509 PMCID: PMC8640478 DOI: 10.1016/j.heliyon.2021.e08480] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/06/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022] Open
Abstract
Fungi have great prospects for synthesis, applications and developing new products in nanotechnology. In recent times, fungi use in nanotechnology is gaining more attention because of the ecological friendly state of their metabolite-mediated nanoparticles, their safety, amenability and applications in diverse fields. The diversity of the metabolites such as enzymes, polysaccharide, polypeptide, protein and other macro-molecules has made fungi a veritable tool for nanoparticles synthesis. Mechanism of fungal nano-biosynthesis from the molecular perspective has been extensively studied through various investigations on its green synthesized metal nanoparticles. Fungal nanobiotechnology has been applied in agricultural, medical and industrial sectors for goods and services improvement and delivery to mankind. Agriculturally, it has found applications in plant disease management and production of environmentally friendly, non-toxic insecticides, fungicides to enhance agricultural production in general. Medically, diagnosis and treatment of diseases, especially of microbial origin have been improved with fungal nanoparticles through more efficient drug delivery systems with great benefits to pharmaceutical industries. This review therefore explored fungal nanobiotechnology; mechanism of synthesis, characterization and potential applications in various fields of human endeavours for goods and services delivery.
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Affiliation(s)
- Elijah A. Adebayo
- Department of Pure and Applied Biology, Ladoke Akintola University, P.M.B 4000, Ogbomoso, Nigeria
- LAUTECH Nanotechnology Research Group, Nigeria
| | - Musibau A. Azeez
- Department of Pure and Applied Biology, Ladoke Akintola University, P.M.B 4000, Ogbomoso, Nigeria
- LAUTECH Nanotechnology Research Group, Nigeria
| | - Micheal B. Alao
- Department of Pure and Applied Biology, Ladoke Akintola University, P.M.B 4000, Ogbomoso, Nigeria
| | - Abel M. Oke
- Department of Pure and Applied Biology, Ladoke Akintola University, P.M.B 4000, Ogbomoso, Nigeria
| | - Daniel A. Aina
- Department of Microbiology, Babcock University, Ilishan-Remo, Ogun State, Nigeria
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Zheng H, Zhang S, Yuan J, Qin T, Li T, Sun Y, Liu X, Wong DKY. Amplified detection signal at a photoelectrochemical aptasensor with a poly(diphenylbutadiene)-BiOBr heterojunction and Au-modified CeO 2 octahedrons. Biosens Bioelectron 2021; 197:113742. [PMID: 34740121 DOI: 10.1016/j.bios.2021.113742] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/04/2021] [Accepted: 10/26/2021] [Indexed: 01/08/2023]
Abstract
A major aspect of this work is the synergistic application of a poly(diphenylbutadiene)-BiOBr composite and a gold nanoparticle-linked CeO2 octahedron to develop a photoelectrochemical aptasensor with an easily measurable detection signal change. Specifically, poly(diphenylbutadiene) nanofiber-immobilised BiOBr flower-like microspheres were developed as a hybrid material with a heterojunction that facilitates high visible light absorption and efficient photo-generated charge separation, which are essential features for sensitive photoelectrochemical sensors. The model analyte acetamiprid was attached via its specific aptamer on the aptasensor. Separately, a gold nanoparticle-linked CeO2 octahedron was strategically used to significantly diminish the photocurrent by impeding electron transfer at the aptasensor surface. After acetamiprid binding, the CeO2 octahedrons were displaced from the aptasensor. This caused a weakened quenching effect and restored the photocurrent to accomplish an "on-off-on" detection mechanism. This photoelectrochemical aptasensor exhibited a detection limit of 0.05 pM over a linear range of 0.1 pM-10 μM acetamiprid. The use of an aptamer has provided good specificity to acetamiprid and anti-interference. In addition, an ∼5.8% relative standard deviation was estimated as the reproducibility of the photoelectrochemical aptasensor. Furthermore, nearly 90% of the initial photocurrent was still measurable after storing these aptasensors at room temperature for 4 weeks, demonstrating their stability.
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Affiliation(s)
- Hejie Zheng
- Henan Joint International Research Laboratory of Environmental Pollution Control Materials, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan Province, 475004, PR China
| | - Si Zhang
- Henan Joint International Research Laboratory of Environmental Pollution Control Materials, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan Province, 475004, PR China
| | - Jiangfeng Yuan
- Henan Joint International Research Laboratory of Environmental Pollution Control Materials, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan Province, 475004, PR China
| | - Tengteng Qin
- Henan Joint International Research Laboratory of Environmental Pollution Control Materials, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan Province, 475004, PR China
| | - Tongtong Li
- Henan Joint International Research Laboratory of Environmental Pollution Control Materials, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan Province, 475004, PR China
| | - Yuping Sun
- Henan Joint International Research Laboratory of Environmental Pollution Control Materials, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan Province, 475004, PR China
| | - Xiaoqiang Liu
- Henan Joint International Research Laboratory of Environmental Pollution Control Materials, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan Province, 475004, PR China.
| | - Danny K Y Wong
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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Chelliah R, Wei S, Daliri EBM, Rubab M, Elahi F, Yeon SJ, Jo KH, Yan P, Liu S, Oh DH. Development of Nanosensors Based Intelligent Packaging Systems: Food Quality and Medicine. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1515. [PMID: 34201071 PMCID: PMC8226856 DOI: 10.3390/nano11061515] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/02/2022]
Abstract
The issue of medication noncompliance has resulted in major risks to public safety and financial loss. The new omnipresent medicine enabled by the Internet of things offers fascinating new possibilities. Additionally, an in-home healthcare station (IHHS), it is necessary to meet the rapidly increasing need for routine nursing and on-site diagnosis and prognosis. This article proposes a universal and preventive strategy to drug management based on intelligent and interactive packaging (I2Pack) and IMedBox. The controlled delamination material (CDM) seals and regulates wireless technologies in novel medicine packaging. As such, wearable biomedical sensors may capture a variety of crucial parameters via wireless communication. On-site treatment and prediction of these critical factors are made possible by high-performance architecture. The user interface is also highlighted to make surgery easier for the elderly, disabled, and patients. Land testing incorporates and validates an approach for prototyping I2Pack and iMedBox. Additionally, sustainability, increased product safety, and quality standards are crucial throughout the life sciences. To achieve these standards, intelligent packaging is also used in the food and pharmaceutical industries. These technologies will continuously monitor the quality of a product and communicate with the user. Data carriers, indications, and sensors are the three most important groups. They are not widely used at the moment, although their potential is well understood. Intelligent packaging should be used in these sectors and the functionality of the systems and the values presented in this analysis.
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Affiliation(s)
- Ramachandran Chelliah
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea; (E.B.-M.D.); (F.E.); (S.-J.Y.); (K.h.J.); (P.Y.)
| | - Shuai Wei
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Products Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Marine Food, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang 524088, China;
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Eric Banan-Mwine Daliri
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea; (E.B.-M.D.); (F.E.); (S.-J.Y.); (K.h.J.); (P.Y.)
| | - Momna Rubab
- School of Food and Agricultural Sciences, University of Management and Technology, Lahore 54770, Pakistan;
| | - Fazle Elahi
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea; (E.B.-M.D.); (F.E.); (S.-J.Y.); (K.h.J.); (P.Y.)
| | - Su-Jung Yeon
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea; (E.B.-M.D.); (F.E.); (S.-J.Y.); (K.h.J.); (P.Y.)
| | - Kyoung hee Jo
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea; (E.B.-M.D.); (F.E.); (S.-J.Y.); (K.h.J.); (P.Y.)
| | - Pianpian Yan
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea; (E.B.-M.D.); (F.E.); (S.-J.Y.); (K.h.J.); (P.Y.)
| | - Shucheng Liu
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Products Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Marine Food, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang 524088, China;
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Deog Hwan Oh
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea; (E.B.-M.D.); (F.E.); (S.-J.Y.); (K.h.J.); (P.Y.)
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Mathematical Modelling of Biosensing Platforms Applied for Environmental Monitoring. CHEMOSENSORS 2021. [DOI: 10.3390/chemosensors9030050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In recent years, mathematical modelling has known an overwhelming integration in different scientific fields. In general, modelling is used to obtain new insights and achieve more quantitative and qualitative information about systems by programming language, manipulating matrices, creating algorithms and tracing functions and data. Researchers have been inspired by these techniques to explore several methods to solve many problems with high precision. In this direction, simulation and modelling have been employed for the development of sensitive and selective detection tools in different fields including environmental control. Emerging pollutants such as pesticides, heavy metals and pharmaceuticals are contaminating water resources, thus threatening wildlife. As a consequence, various biosensors using modelling have been reported in the literature for efficient environmental monitoring. In this review paper, the recent biosensors inspired by modelling and applied for environmental monitoring will be overviewed. Moreover, the level of success and the analytical performances of each modelling-biosensor will be discussed. Finally, current challenges in this field will be highlighted.
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Rai M, Bonde S, Golinska P, Trzcińska-Wencel J, Gade A, Abd-Elsalam KA, Shende S, Gaikwad S, Ingle AP. Fusarium as a Novel Fungus for the Synthesis of Nanoparticles: Mechanism and Applications. J Fungi (Basel) 2021; 7:139. [PMID: 33672011 PMCID: PMC7919287 DOI: 10.3390/jof7020139] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/06/2021] [Accepted: 02/10/2021] [Indexed: 01/05/2023] Open
Abstract
Nanotechnology is a new and developing branch that has revolutionized the world by its applications in various fields including medicine and agriculture. In nanotechnology, nanoparticles play an important role in diagnostics, drug delivery, and therapy. The synthesis of nanoparticles by fungi is a novel, cost-effective and eco-friendly approach. Among fungi, Fusarium spp. play an important role in the synthesis of nanoparticles and can be considered as a nanofactory for the fabrication of nanoparticles. The synthesis of silver nanoparticles (AgNPs) from Fusarium, its mechanism and applications are discussed in this review. The synthesis of nanoparticles from Fusarium is the biogenic and green approach. Fusaria are found to be a versatile biological system with the ability to synthesize nanoparticles extracellularly. Different species of Fusaria have the potential to synthesise nanoparticles. Among these, F. oxysporum has demonstrated a high potential for the synthesis of AgNPs. It is hypothesised that NADH-dependent nitrate reductase enzyme secreted by F. oxysporum is responsible for the reduction of aqueous silver ions into AgNPs. The toxicity of nanoparticles depends upon the shape, size, surface charge, and the concentration used. The nanoparticles synthesised by different species of Fusaria can be used in medicine and agriculture.
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Affiliation(s)
- Mahendra Rai
- Department of Biotechnology, Nanobiotechnology Laboratory, Sant Gadge Baba Amravati University, Amravati 444602, India; (S.B.); (A.G.); (S.S.)
- Department of Microbiology, Nicolaus Copernicus University, Lwowska, 87-100 Torun, Poland; (P.G.); (J.T.-W.)
| | - Shital Bonde
- Department of Biotechnology, Nanobiotechnology Laboratory, Sant Gadge Baba Amravati University, Amravati 444602, India; (S.B.); (A.G.); (S.S.)
| | - Patrycja Golinska
- Department of Microbiology, Nicolaus Copernicus University, Lwowska, 87-100 Torun, Poland; (P.G.); (J.T.-W.)
| | - Joanna Trzcińska-Wencel
- Department of Microbiology, Nicolaus Copernicus University, Lwowska, 87-100 Torun, Poland; (P.G.); (J.T.-W.)
| | - Aniket Gade
- Department of Biotechnology, Nanobiotechnology Laboratory, Sant Gadge Baba Amravati University, Amravati 444602, India; (S.B.); (A.G.); (S.S.)
| | - Kamel A. Abd-Elsalam
- Agricultural Research Center, Plant Pathology Research Institute, Giza 12619, Egypt;
| | - Sudhir Shende
- Department of Biotechnology, Nanobiotechnology Laboratory, Sant Gadge Baba Amravati University, Amravati 444602, India; (S.B.); (A.G.); (S.S.)
- Academy of Biology and Biotechnology, Southern Federal University, 344006 Rostov-on-Don, Russia
| | - Swapnil Gaikwad
- Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth (Deemed to be University), Tathawade, Pune 411033, India;
| | - Avinash P. Ingle
- Biotechnology Centre, Department of Agricultural Botany, Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, Maharashtra 444104, India;
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Sahoo M, Vishwakarma S, Panigrahi C, Kumar J. Nanotechnology: Current applications and future scope in food. FOOD FRONTIERS 2020. [DOI: 10.1002/fft2.58] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Monalisa Sahoo
- Centre for Rural Development and Technology Indian Institute of Technology Delhi New Delhi India
| | - Siddharth Vishwakarma
- Agricultural and Food Engineering Department Indian Institute of Technology Kharagpur Kharagpur India
| | - Chirasmita Panigrahi
- Agricultural and Food Engineering Department Indian Institute of Technology Kharagpur Kharagpur India
| | - Jayant Kumar
- Agricultural and Food Engineering Department Indian Institute of Technology Kharagpur Kharagpur India
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Kumar V, Guleria P. Application of DNA-Nanosensor for Environmental Monitoring: Recent Advances and Perspectives. CURRENT POLLUTION REPORTS 2020:1-21. [PMID: 33344145 PMCID: PMC7732738 DOI: 10.1007/s40726-020-00165-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/04/2020] [Indexed: 05/24/2023]
Abstract
PURPOSE OF REVIEW Environmental pollutants are threat to human beings. Pollutants can lead to human health and environment hazards. The purpose of this review is to summarize the work done on detection of environmental pollutants using DNA nanosensors and challenges in the areas that can be focused for safe environment. RECENT FINDINGS Most of the DNA-based nanosensors designed so far use DNA as recognition element. ssDNA, dsDNA, complementary mismatched DNA, aptamers, and G-quadruplex DNA are commonly used as probes in nanosensors. More and more DNA sequences are being designed that can specifically detect various pollutants even simultaneously in complex milk, wastewater, soil, blood, tap water, river, and pond water samples. The feasibility of direct detection, ease of designing, and analysis makes DNA nanosensors fit for future point-of-care applications. SUMMARY DNA nanosensors are easy to design and have good sensitivity. DNA component and nanomaterials can be designed in a controlled manner to detect various environmental pollutants. This review identifies the recent advances in DNA nanosensor designing and opportunities available to design nanosensors for unexplored pathogens, antibiotics, pesticides, GMO, heavy metals, and other toxic pollutant.
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Affiliation(s)
- Vineet Kumar
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University (LPU), Jalandhar – Delhi G.T. Road, Phagwara, Punjab 144411 India
| | - Praveen Guleria
- Department of Biotechnology, Faculty of Life Sciences, DAV University, Jalandhar, Punjab 144012 India
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Khoshbin Z, Housaindokht MR, Izadyar M, Bozorgmehr MR, Verdian A. Recent advances in computational methods for biosensor design. Biotechnol Bioeng 2020; 118:555-578. [PMID: 33135778 DOI: 10.1002/bit.27618] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/25/2020] [Accepted: 10/29/2020] [Indexed: 01/20/2023]
Abstract
Biosensors are analytical tools with a great application in healthcare, food quality control, and environmental monitoring. They are of considerable interest to be designed by using cost-effective and efficient approaches. Designing biosensors with improved functionality or application in new target detection has been converted to a fast-growing field of biomedicine and biotechnology branches. Experimental efforts have led to valuable successes in the field of biosensor design; however, some deficiencies restrict their utilization for this purpose. Computational design of biosensors is introduced as a promising key to eliminate the gap. A set of reliable structure prediction of the biosensor segments, their stability, and accurate descriptors of molecular interactions are required to computationally design biosensors. In this review, we provide a comprehensive insight into the progress of computational methods to guide the design and development of biosensors, including molecular dynamics simulation, quantum mechanics calculations, molecular docking, virtual screening, and a combination of them as the hybrid methodologies. By relying on the recent advances in the computational methods, an opportunity emerged for them to be complementary or an alternative to the experimental methods in the field of biosensor design.
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Affiliation(s)
- Zahra Khoshbin
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Mohammad Izadyar
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Asma Verdian
- Department of Food Safety and Quality Control, Research Institute of Food Science and Technology (RIFST), Mashhad, Iran
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Buglak AA, Samokhvalov AV, Zherdev AV, Dzantiev BB. Methods and Applications of In Silico Aptamer Design and Modeling. Int J Mol Sci 2020; 21:E8420. [PMID: 33182550 PMCID: PMC7698023 DOI: 10.3390/ijms21228420] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/04/2020] [Accepted: 11/08/2020] [Indexed: 02/07/2023] Open
Abstract
Aptamers are nucleic acid analogues of antibodies with high affinity to different targets, such as cells, viruses, proteins, inorganic materials, and coenzymes. Empirical approaches allow the design of in vitro aptamers that bind particularly to a target molecule with high affinity and selectivity. Theoretical methods allow significant expansion of the possibilities of aptamer design. In this study, we review theoretical and joint theoretical-experimental studies dedicated to aptamer design and modeling. We consider aptamers with different targets, such as proteins, antibiotics, organophosphates, nucleobases, amino acids, and drugs. During nucleic acid modeling and in silico design, a full set of in silico methods can be applied, such as docking, molecular dynamics (MD), and statistical analysis. The typical modeling workflow starts with structure prediction. Then, docking of target and aptamer is performed. Next, MD simulations are performed, which allows for an evaluation of the stability of aptamer/ligand complexes and determination of the binding energies with higher accuracy. Then, aptamer/ligand interactions are analyzed, and mutations of studied aptamers made. Subsequently, the whole procedure of molecular modeling can be reiterated. Thus, the interactions between aptamers and their ligands are complex and difficult to understand using only experimental approaches. Docking and MD are irreplaceable when aptamers are studied in silico.
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Affiliation(s)
- Andrey A. Buglak
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky prospect 33, 119071 Moscow, Russia; (A.V.S.); (A.V.Z.); (B.B.D.)
- Physical Faculty, St. Petersburg State University, 7/9 Universitetskaya naberezhnaya, 199034 St. Petersburg, Russia
| | - Alexey V. Samokhvalov
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky prospect 33, 119071 Moscow, Russia; (A.V.S.); (A.V.Z.); (B.B.D.)
| | - Anatoly V. Zherdev
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky prospect 33, 119071 Moscow, Russia; (A.V.S.); (A.V.Z.); (B.B.D.)
| | - Boris B. Dzantiev
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky prospect 33, 119071 Moscow, Russia; (A.V.S.); (A.V.Z.); (B.B.D.)
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Navien TN, Thevendran R, Hamdani HY, Tang TH, Citartan M. In silico molecular docking in DNA aptamer development. Biochimie 2020; 180:54-67. [PMID: 33086095 DOI: 10.1016/j.biochi.2020.10.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/23/2020] [Accepted: 10/14/2020] [Indexed: 12/21/2022]
Abstract
Aptamers are single-stranded DNA or RNA oligonucleotides generated by SELEX that exhibit binding affinity and specificity against a wide variety of target molecules. Compared to RNA aptamers, DNA aptamers are much more stable and therefore are widely adopted in a number of applications especially in diagnostics. The tediousness and rigor associated with certain steps of the SELEX intensify the efforts to adopt in silico molecular docking approaches together with in vitro SELEX procedures in developing DNA aptamers. Inspired by these endeavors, we carry out an overview of the in silico molecular docking approaches in DNA aptamer generation, by detailing the stepwise procedures as well as shedding some light on the various softwares used. The in silico maturation strategy and the limitations of the in silico approaches are also underscored.
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Affiliation(s)
- Tholasi Nadhan Navien
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Ramesh Thevendran
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Hazrina Yusof Hamdani
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Thean-Hock Tang
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
| | - Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
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Huo B, Hu Y, Gao Z, Li G. Recent advances on functional nucleic acid-based biosensors for detection of food contaminants. Talanta 2020; 222:121565. [PMID: 33167261 DOI: 10.1016/j.talanta.2020.121565] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 08/17/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023]
Abstract
It has seen increasing development of reliable, robust, and flexible biosensors for rapid food-safety analysis in the past few decades. Recently, functional nucleic acid-based biosensors have attracted attention because of their programmability, bottom-up characteristics, and structural switches. However, few systematic reviews devoted to categorizing the potential of DNA nanostructures and devices were found for detecting food contaminants. Hence, the applications of functional nucleic acid-based biosensors were reviewed for analyzing food contaminants, including foodborne pathogen bacteria, biotoxins, heavy metals, and et al. In addition to categorizing the various biosensors, multiple signal readout strategies, such as optical, electrochemical, and mass-based signals were also examined. Finally, the future changes and potential opportunities, as well as practical applications of functional nucleic acid-based biosensors were discussed.
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Affiliation(s)
- Bingyang Huo
- School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yuling Hu
- School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Gongke Li
- School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China.
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Shende P, Prabhakar B, Patil A. Color changing sensors: A multimodal system for integrated screening. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115687] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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17
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Aptasensors for pesticide detection. Biosens Bioelectron 2019; 130:174-184. [PMID: 30738246 DOI: 10.1016/j.bios.2019.01.006] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/05/2019] [Accepted: 01/12/2019] [Indexed: 12/16/2022]
Abstract
Pesticide contamination has become one of the most serious problems of public health in the world, due to their wide application in agriculture industry to guarantee the crop yield and quality. The detection of pesticide residues plays an important role in food safety management and environment protection. However, the conventional detection methodologies cannot realize highly sensitive, selective and on-site detection, which limits their applications. Aptamers are short single-stranded oligonucleotides (RNA or DNA) selected by SELEX method, which can selectively bind to their targets with high affinity. Compared with the commonly used antibodies or enzymes in designing biosensors, aptamers exhibit better stability, low molecular weight, easy modification and low cost, and were regarded as excellent candidates for developing aptasensors for pesticide detection. In this review, application of aptamers for pesticide detection was reviewed. Firstly, aptamers specifically bind to various pesticides were first summarized. Secondly, the progresses and highlights of developing aptasensors for highly-sensitive and selective detection of pesticide residues were systematically provided. Finally, the present challenges and future perspectives for developing novel highly-effective aptasensor for the detection of pesticide residues were discussed.
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He X, Deng H, Hwang HM. The current application of nanotechnology in food and agriculture. J Food Drug Anal 2019; 27:1-21. [PMID: 30648562 PMCID: PMC9298627 DOI: 10.1016/j.jfda.2018.12.002] [Citation(s) in RCA: 266] [Impact Index Per Article: 53.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 12/25/2022] Open
Abstract
The rapid development of nanotechnology has been facilitating the transformations of traditional food and agriculture sectors, particularly the invention of smart and active packaging, nanosensors, nanopesticides and nanofertilizers. Numerous novel nanomaterials have been developed for improving food quality and safety, crop growth, and monitoring environmental conditions. In this review the most recent trends in nanotechnology are discussed and the most challenging tasks and promising opportunities in the food and agriculture sectors from selected recent studies are addressed. The toxicological fundamentals and risk assessment of nanomaterials in these new food and agriculture products are also discussed. We highlighted the potential application of bio-synthesized and bio-inspired nanomaterial for sustainable development. However, fundamental questions with regard to high performance, low toxic nanomaterials need to be addressed to fuel active development and application of nanotechnology. Regulation and legislation are also paramount to regulating the manufacturing, processing, application, as well as disposal of nanomaterials. Efforts are still needed to strengthen public awareness and acceptance of the novel nano-enabled food and agriculture products. We conclude that nanotechnology offers a plethora of opportunities, by providing a novel and sustainable alternative in the food and agriculture sectors.
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Affiliation(s)
- Xiaojia He
- The University of Georgia, Athens, GA, 30602,
USA
| | - Hua Deng
- Morgan State University, Baltimore, MD, 21251,
USA
| | - Huey-min Hwang
- Jackson State University, Jackson, MS, 39217,
USA
- Dalian Marinetime University, Dalian, Liaoning,
China
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Shahbaaz M, Kanchi S, Sabela M, Bisetty K. Structural basis of pesticide detection by enzymatic biosensing: a molecular docking and MD simulation study. J Biomol Struct Dyn 2017; 36:1402-1416. [PMID: 28463066 DOI: 10.1080/07391102.2017.1323673] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Designing of rapid, facile, selective, and cost-effective biosensor technology is a growing area for the detection of various classes of pesticides. The biosensor with these features can be achieved only through the various bio-components using different transducers. This study, therefore, focuses on the usage of molecular docking, specificity tendencies, and capabilities of proteins for the detection of pesticides. Accordingly, the four transducers, acetylcholinesterase (ACH), cytochromes P450 (CYP), glutathione S-transferase (GST), and protein kinase C (PKC) were selected based on their applications including neurotransmitter, metabolism, detoxification enzyme, and protein phosphorylation. Then after molecular docking of the pesticides, fenobucarb, dichlorodiphenyltrichloroethane (DDT), and parathion onto each enzyme, the conformational behavior of the most stable complexes was further analyzed using 50 ns Molecular Dynamics (MD) simulations carried out under explicit water conditions. In the case of protein kinase C (PKC) and cytochrome P450 3A4 enzyme (CYP), the fenobucarb complex showed the most suitable combination of free energy of binding and inhibition constant -4.42 kcal/mol (573.73 μM) and -5.1 kcal/mol (183.49 μM), respectively. Parathion dominated for acetylcholinesterase (ACH) with -4.57 kcal/mol (448.09 μM) and lastly dichlorodiphenyltrichloroethane for glutathione S-transferase (GST), -5.43 kcal/mol (103.88 μM). The RMSD variations were critical for understanding the impact of pesticides as they distinctively influence the energetic attributes of the proteins. Overall, the outcomes from the extensive analysis provide an insight into the structural features of the proteins studied, thereby highlighting their potential use as a substrate in biorecognition sensing of pesticide compounds.
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Affiliation(s)
- Mohd Shahbaaz
- a Department of Chemistry , Durban University of Technology , Durban 4000 , South Africa
| | - Suvardhan Kanchi
- a Department of Chemistry , Durban University of Technology , Durban 4000 , South Africa
| | - Myalowenkosi Sabela
- a Department of Chemistry , Durban University of Technology , Durban 4000 , South Africa
| | - Krishna Bisetty
- a Department of Chemistry , Durban University of Technology , Durban 4000 , South Africa
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Biosensors and their applications in detection of organophosphorus pesticides in the environment. Arch Toxicol 2016; 91:109-130. [DOI: 10.1007/s00204-016-1875-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 10/10/2016] [Indexed: 01/08/2023]
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