1
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Hasanzadeh A, Ebadati A, Saeedi S, Kamali B, Noori H, Jamei B, Hamblin MR, Liu Y, Karimi M. Nucleic acid-responsive smart systems for controlled cargo delivery. Biotechnol Adv 2024; 74:108393. [PMID: 38825215 DOI: 10.1016/j.biotechadv.2024.108393] [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: 08/21/2023] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
Stimulus-responsive delivery systems allow controlled, highly regulated, and efficient delivery of various cargos while minimizing side effects. Owing to the unique properties of nucleic acids, including the ability to adopt complex structures by base pairing, their easy synthesis, high specificity, shape memory, and configurability, they have been employed in autonomous molecular motors, logic circuits, reconfigurable nanoplatforms, and catalytic amplifiers. Moreover, the development of nucleic acid (NA)-responsive intelligent delivery vehicles is a rapidly growing field. These vehicles have attracted much attention in recent years due to their programmable, controllable, and reversible properties. In this work, we review several types of NA-responsive controlled delivery vehicles based on locks and keys, including DNA/RNA-responsive, aptamer-responsive, and CRISPR-responsive, and summarize their advantages and limitations.
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Affiliation(s)
- Akbar Hasanzadeh
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Arefeh Ebadati
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Department of Molecular and Cell Biology, University of California, Merced, Merced, USA
| | - Sara Saeedi
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Babak Kamali
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Noori
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Behnam Jamei
- Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa
| | - Yong Liu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China.
| | - Mahdi Karimi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Oncopathology Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran; Research Center for Science and Technology in Medicine, Tehran University of Medical Sciences, Tehran, Iran; Applied Biotechnology Research Centre, Tehran Medical Science, Islamic Azad University, Tehran, Iran.
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2
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Fallah A, Havaei SA, Sedighian H, Kachuei R, Fooladi AAI. Prediction of aptamer affinity using an artificial intelligence approach. J Mater Chem B 2024. [PMID: 39158322 DOI: 10.1039/d4tb00909f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Aptamers are oligonucleotide sequences that can connect to particular target molecules, similar to monoclonal antibodies. They can be chosen by systematic evolution of ligands by exponential enrichment (SELEX), and are modifiable and can be synthesized. Even if the SELEX approach has been improved a lot, it is frequently challenging and time-consuming to identify aptamers experimentally. In particular, structure-based methods are the most used in computer-aided design and development of aptamers. For this purpose, numerous web-based platforms have been suggested for the purpose of forecasting the secondary structure and 3D configurations of RNAs and DNAs. Also, molecular docking and molecular dynamics (MD), which are commonly utilized in protein compound selection by structural information, are suitable for aptamer selection. On the other hand, from a large number of sequences, artificial intelligence (AI) may be able to quickly discover the possible aptamer candidates. Conversely, sophisticated machine and deep-learning (DL) models have demonstrated efficacy in forecasting the binding properties between ligands and targets during drug discovery; as such, they may provide a reliable and precise method for forecasting the binding of aptamers to targets. This research looks at advancements in AI pipelines and strategies for aptamer binding ability prediction, such as machine and deep learning, as well as structure-based approaches, molecular dynamics and molecular docking simulation methods.
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Affiliation(s)
- Arezoo Fallah
- Department of Bacteriology and Virology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyed Asghar Havaei
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Hamid Sedighian
- Applied Microbiology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Reza Kachuei
- Molecular Biology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Abbas Ali Imani Fooladi
- Applied Microbiology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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3
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Kumar S, Mohan A, Sharma NR, Kumar A, Girdhar M, Malik T, Verma AK. Computational Frontiers in Aptamer-Based Nanomedicine for Precision Therapeutics: A Comprehensive Review. ACS OMEGA 2024; 9:26838-26862. [PMID: 38947800 PMCID: PMC11209897 DOI: 10.1021/acsomega.4c02466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/09/2024] [Accepted: 05/28/2024] [Indexed: 07/02/2024]
Abstract
In the rapidly evolving landscape of nanomedicine, aptamers have emerged as powerful molecular tools, demonstrating immense potential in targeted therapeutics, diagnostics, and drug delivery systems. This paper explores the computational features of aptamers in nanomedicine, highlighting their advantages over antibodies, including selectivity, low immunogenicity, and a simple production process. A comprehensive overview of the aptamer development process, specifically the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process, sheds light on the intricate methodologies behind aptamer selection. The historical evolution of aptamers and their diverse applications in nanomedicine are discussed, emphasizing their pivotal role in targeted drug delivery, precision medicine and therapeutics. Furthermore, we explore the integration of artificial intelligence (AI), machine learning (ML), Internet of Things (IoT), Internet of Medical Things (IoMT), and nanotechnology in aptameric development, illustrating how these cutting-edge technologies are revolutionizing the selection and optimization of aptamers for tailored biomedical applications. This paper also discusses challenges in computational methods for advancing aptamers, including reliable prediction models, extensive data analysis, and multiomics data incorporation. It also addresses ethical concerns and restrictions related to AI and IoT use in aptamer research. The paper examines progress in computer simulations for nanomedicine. By elucidating the importance of aptamers, understanding their superiority over antibodies, and exploring the historical context and challenges, this review serves as a valuable resource for researchers and practitioners aiming to harness the full potential of aptamers in the rapidly evolving field of nanomedicine.
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Affiliation(s)
- Shubham Kumar
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
| | - Anand Mohan
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
| | - Neeta Raj Sharma
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
| | - Anil Kumar
- Gene
Regulation Laboratory, National Institute
of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Madhuri Girdhar
- Division
of Research and Development, Lovely Professional
University, Phagwara 144401, Punjab, India
| | - Tabarak Malik
- Department
of Biomedical Sciences, Institute of Health, Jimma University, MVJ4+R95 Jimma, Ethiopia
| | - Awadhesh Kumar Verma
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
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4
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Thanaskody K, Natashah FN, Nordin F, Kamarul Zaman WSW, Tye GJ. Designing molecules: directing stem cell differentiation. Front Bioeng Biotechnol 2024; 12:1396405. [PMID: 38803845 PMCID: PMC11129639 DOI: 10.3389/fbioe.2024.1396405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
Stem cells have been widely applied in regenerative and therapeutic medicine for their unique regenerative properties. Although much research has shown their potential, it remains tricky in directing stem cell differentiation. The advancement of genetic and therapeutic technologies, however, has facilitated this issue through development of design molecules. These molecules are designed to overcome the drawbacks previously faced, such as unexpected differentiation outcomes and insufficient migration of endogenous or exogenous MSCs. Here, we introduced aptamer, bacteriophage, and biological vectors as design molecules and described their characteristics. The methods of designing/developing discussed include various Systematic Evolution of Ligands by Exponential Enrichment (SELEX) procedures, in silico approaches, and non-SELEX methods for aptamers, and genetic engineering methods such as homologous recombination, Bacteriophage Recombineering of Electroporated DNA (BRED), Bacteriophage Recombineering with Infectious Particles (BRIP), and genome rebooting for bacteriophage. For biological vectors, methods such as alternate splicing, multiple promoters, internal ribosomal entry site, CRISPR-Cas9 system and Cre recombinase mediated recombination were used to design viral vectors, while non-viral vectors like exosomes are generated through parental cell-based direct engineering. Besides that, we also discussed the pros and cons, and applications of each design molecule in directing stem cell differentiation to illustrate their great potential in stem cells research. Finally, we highlighted some safety and efficacy concerns to be considered for future studies.
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Affiliation(s)
- Kalaiselvaan Thanaskody
- Centre for Tissue Engineering and Regenerative Medicine (CTERM), Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
| | - Fajriyah Nur Natashah
- Centre for Tissue Engineering and Regenerative Medicine (CTERM), Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
| | - Fazlina Nordin
- Centre for Tissue Engineering and Regenerative Medicine (CTERM), Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
| | - Wan Safwani Wan Kamarul Zaman
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur, Malaysia
- Centre for Innovation in Medical Engineering (CIME), Department of Biomedical Engineering, Faculty of Engineering, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Gee Jun Tye
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
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5
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Cossettini A, Pasquardini L, Romani A, Feriani A, Pinamonti D, Manzano M. Computational aptamer design for spike glycoprotein (S) (SARS CoV-2) detection with an electrochemical aptasensor. Appl Microbiol Biotechnol 2024; 108:259. [PMID: 38470514 PMCID: PMC10933206 DOI: 10.1007/s00253-024-13066-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 02/05/2024] [Accepted: 02/11/2024] [Indexed: 03/14/2024]
Abstract
A new bioinformatic platform (APTERION) was used to design in a short time and with high specificity an aptamer for the detection of the spike protein, a structural protein of SARS-CoV-2 virus, responsible for the COVID-19 pandemic. The aptamer concentration on the carbon electrode surface was optimized using static contact angle and fluorescence method, while specificity was tested using differential pulse voltammetry (DPV) associated to carbon screen-printed electrodes. The data obtained demonstrated the good features of the aptamer which could be used to create a rapid method for the detection of SARS-CoV-2 virus. In fact, it is specific for spike also when tested against bovine serum albumin and lysozyme, competitor proteins if saliva is used as sample to test for the virus presence. Spectrofluorometric characterization allowed to measure the amount of aptamer present on the carbon electrode surface, while DPV measurements proved the affinity of the aptamer towards the spike protein and gave quantitative results. The acquired data allowed to conclude that the APTERION bioinformatic platform is a good method for aptamer design for rapidity and specificity. KEY POINTS: • Spike protein detection using an electrochemical biosensor • Aptamer characterization by contact angle and fluorescent measurements on electrode surface • Computational design of specific aptamers to speed up the aptameric sequence time.
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Affiliation(s)
- Alessia Cossettini
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Via Sondrio 2/A, 33100, Udine, Italy
| | | | | | - Aldo Feriani
- Arta Peptidion srls, Via Quasimodo 11, 43126, Parma, Italy
| | - Debora Pinamonti
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Via Sondrio 2/A, 33100, Udine, Italy
| | - Marisa Manzano
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Via Sondrio 2/A, 33100, Udine, Italy.
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6
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Chen L, Yu Z, Wu Z, Zhou M, Wang Y, Yu X, Li W, Liu G, Tang Y. AptaDB: a comprehensive database integrating aptamer-target interactions. RNA (NEW YORK, N.Y.) 2024; 30:189-199. [PMID: 38164624 PMCID: PMC10870366 DOI: 10.1261/rna.079784.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
Aptamers have emerged as research hotspots of the next generation due to excellent performance benefits and application potentials in pharmacology, medicine, and analytical chemistry. Despite the numerous aptamer investigations, the lack of comprehensive data integration has hindered the development of computational methods for aptamers and the reuse of aptamers. A public access database named AptaDB, derived from experimentally validated data manually collected from the literature, was hence developed, integrating comprehensive aptamer-related data, which include six key components: (i) experimentally validated aptamer-target interaction information, (ii) aptamer property information, (iii) structure information of aptamer, (iv) target information, (v) experimental activity information, and (vi) algorithmically calculated similar aptamers. AptaDB currently contains 1350 experimentally validated aptamer-target interactions, 1230 binding affinity constants, 1293 aptamer sequences, and more. Compared to other aptamer databases, it contains twice the number of entries found in available databases. The collection and integration of the above information categories is unique among available aptamer databases and provides a user-friendly interface. AptaDB will also be continuously updated as aptamer research evolves. We expect that AptaDB will become a powerful source for aptamer rational design and a valuable tool for aptamer screening in the future. For access to AptaDB, please visit http://lmmd.ecust.edu.cn/aptadb/.
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Affiliation(s)
- Long Chen
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhuohang Yu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zengrui Wu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Moran Zhou
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yimeng Wang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xinxin Yu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yun Tang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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7
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Yang J, Lu X, Chen M, Tang C, Wei Z, Liu Y, Jiang H, Yu P. Non-immobilized GO-SELEX screening of aptamers against cyclosporine A and its application in a AuNPs colorimetric aptasensor. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:227-236. [PMID: 38105729 DOI: 10.1039/d3ay01775c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Cyclosporine A (CsA) is an immunosuppressive drug that is widely used in clinical practice. Due to its narrow therapeutic window and the significant differences between individuals, the therapeutic drug monitoring (TDM) of CsA is required to ensure patient safety. In this study, we screened a novel aptamer, named CsA7, which could specifically recognize CsA, and developed a AuNPs colorimetric aptasensor for the rapid detection of CsA. In the SELEX process, after eight rounds of screening, four aptamer candidate sequences were obtained and subjected to binding affinity and specificity tests. Finally, the CsA7 aptamer (Kd = 41.21 ng mL-1) showed the highest affinity for CsA. Based on CsA7, we also developed a AuNPs colorimetric aptasensor, which had a detection limit of 0.1 ng mL-1 and a quantitative range of 0.1-500 ng mL-1 and showed good selectivity among CsA and its analogs. According to the results, the CsA7 aptamer provides an alternative recognition molecule to the antibody in biosensor applications and shows great potential for the rapid and convenient detection of CsA.
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Affiliation(s)
- Jie Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, No. 172, Tongzipo Road, Changsha, Hunan 410013, China.
| | - Xiaoling Lu
- Xiangya School of Pharmaceutical Sciences, Central South University, No. 172, Tongzipo Road, Changsha, Hunan 410013, China.
| | - Meilun Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, No. 172, Tongzipo Road, Changsha, Hunan 410013, China.
| | - Chunhua Tang
- Xiangya School of Pharmaceutical Sciences, Central South University, No. 172, Tongzipo Road, Changsha, Hunan 410013, China.
| | - Zheng Wei
- Xiangya School of Pharmaceutical Sciences, Central South University, No. 172, Tongzipo Road, Changsha, Hunan 410013, China.
| | - Yijie Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, No. 172, Tongzipo Road, Changsha, Hunan 410013, China.
| | - Hanbing Jiang
- Xiangya School of Pharmaceutical Sciences, Central South University, No. 172, Tongzipo Road, Changsha, Hunan 410013, China.
- Xiangya School of Pharmaceutical Sciences, Central South University, No. 1 Traditional Chinese Medicine Hospital in Changde, Hunan Province, China
| | - Peng Yu
- Xiangya School of Pharmaceutical Sciences, Central South University, No. 172, Tongzipo Road, Changsha, Hunan 410013, China.
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Jiao X, Peng X, Jin X, Liu N, Yu Y, Liu R, Li Z. Nano-composite system of traditional Chinese medicine for ocular applications: molecular docking and three-dimensional modeling insight for intelligent drug evaluation. Drug Deliv Transl Res 2023; 13:3132-3144. [PMID: 37355484 DOI: 10.1007/s13346-023-01376-x] [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] [Accepted: 05/30/2023] [Indexed: 06/26/2023]
Abstract
The absorption of drugs was impeded in the posterior part of the eye due to the special structure. In addition, it was crucial to comprehend transport laws of molecules in ocular drug delivery for designing effective strategies. However, the current quality evaluation methods of the eye were backward and lack of dynamic monitoring of drug processes in vivo. Herein, nano-drug delivery system and three-dimensional (3D) model were combined to overcome the problems of low bioavailability and diffusion law. The model drugs were screened by molecular docking. The flexible nano-liposome (FNL) and temperature-sensitive gel (TSG) composite formulation was characterized through comprehensive evaluation. COMSOL software was utilized to build 3D eyeball to predict the bioavailability of drugs. The size of the preparation was about 98.34 nm which is relatively optimal for the enhanced permeability of the eyes. The formulation showed a stronger safety and non-irritant. The pharmacokinetics results of aqueous humor showed that the AUC of two drugs in this system increased by 3.79 and 3.94 times, respectively. The results of 3D calculation model proved that the concentrations of drugs reaching the retina were 1.90×10-5 mol/m3 and 6.37×10-6 mol/m3. In conclusion, the FNL-TSG markedly improved the bioavailability of multiple components in the eye. More importantly, a simplified 3D model was developed to preliminarily forecast the bioavailability of the retina after drug infusion, providing technical support for the accurate evaluation of ocular drug delivery. It provided new pattern for the development of intelligent versatile ophthalmic preparations.
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Affiliation(s)
- Xinyi Jiao
- State Key Laboratory of Component‑Based Chinese Medicine, College of Pharmaceutical Engineering of Traditional Chinese Medicine, Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Xingru Peng
- State Key Laboratory of Component‑Based Chinese Medicine, College of Pharmaceutical Engineering of Traditional Chinese Medicine, Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Xin Jin
- Military Medicine Section, Dongli District, Logistics University of People's Armed Police Force, 1 Huizhihuan Road, Tianjin, 300309, China
| | - Ning Liu
- State Key Laboratory of Component‑Based Chinese Medicine, College of Pharmaceutical Engineering of Traditional Chinese Medicine, Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Yang Yu
- State Key Laboratory of Component‑Based Chinese Medicine, College of Pharmaceutical Engineering of Traditional Chinese Medicine, Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Rui Liu
- State Key Laboratory of Component‑Based Chinese Medicine, College of Pharmaceutical Engineering of Traditional Chinese Medicine, Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Zheng Li
- State Key Laboratory of Component‑Based Chinese Medicine, College of Pharmaceutical Engineering of Traditional Chinese Medicine, Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
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Sequeira-Antunes B, Ferreira HA. Nucleic Acid Aptamer-Based Biosensors: A Review. Biomedicines 2023; 11:3201. [PMID: 38137422 PMCID: PMC10741014 DOI: 10.3390/biomedicines11123201] [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: 10/20/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Aptamers, short strands of either DNA, RNA, or peptides, known for their exceptional specificity and high binding affinity to target molecules, are providing significant advancements in the field of health. When seamlessly integrated into biosensor platforms, aptamers give rise to aptasensors, unlocking a new dimension in point-of-care diagnostics with rapid response times and remarkable versatility. As such, this review aims to present an overview of the distinct advantages conferred by aptamers over traditional antibodies as the molecular recognition element in biosensors. Additionally, it delves into the realm of specific aptamers made for the detection of biomarkers associated with infectious diseases, cancer, cardiovascular diseases, and metabolomic and neurological disorders. The review further elucidates the varying binding assays and transducer techniques that support the development of aptasensors. Ultimately, this review discusses the current state of point-of-care diagnostics facilitated by aptasensors and underscores the immense potential of these technologies in advancing the landscape of healthcare delivery.
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Affiliation(s)
- Beatriz Sequeira-Antunes
- Institute of Biophysics and Biomedical Engineering, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
- Exotictarget, 4900-378 Viana do Castelo, Portugal
- Instituto de Engenharia de Sistemas e Computadores-Microsistemas e Nanotecnologias (INESC-MN), 1000-029 Lisbon, Portugal
| | - Hugo Alexandre Ferreira
- Institute of Biophysics and Biomedical Engineering, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
- Exotictarget, 4900-378 Viana do Castelo, Portugal
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10
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Troisi R, Balasco N, Autiero I, Vitagliano L, Sica F. Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies. Int J Mol Sci 2023; 24:16318. [PMID: 38003510 PMCID: PMC10671752 DOI: 10.3390/ijms242216318] [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: 10/20/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Aptamers are synthetic nucleic acids that are developed to target with high affinity and specificity chemical entities ranging from single ions to macromolecules and present a wide range of chemical and physical properties. Their ability to selectively bind proteins has made these compounds very attractive and versatile tools, in both basic and applied sciences, to such an extent that they are considered an appealing alternative to antibodies. Here, by exhaustively surveying the content of the Protein Data Bank (PDB), we review the structural aspects of the protein-aptamer recognition process. As a result of three decades of structural studies, we identified 144 PDB entries containing atomic-level information on protein-aptamer complexes. Interestingly, we found a remarkable increase in the number of determined structures in the last two years as a consequence of the effective application of the cryo-electron microscopy technique to these systems. In the present paper, particular attention is devoted to the articulated architectures that protein-aptamer complexes may exhibit. Moreover, the molecular mechanism of the binding process was analyzed by collecting all available information on the structural transitions that aptamers undergo, from their protein-unbound to the protein-bound state. The contribution of computational approaches in this area is also highlighted.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Nicole Balasco
- Institute of Molecular Biology and Pathology, CNR c/o Department of Chemistry, University of Rome Sapienza, 00185 Rome, Italy;
| | - Ida Autiero
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
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11
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Alfinito E. TBA for Sensing Toxic Cations: A Critical Analysis of Structural and Electrical Properties. Int J Mol Sci 2023; 24:14492. [PMID: 37833940 PMCID: PMC10572628 DOI: 10.3390/ijms241914492] [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: 08/16/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Food and drinks can be contaminated with pollutants such as lead and strontium, which poses a serious danger to human health. For this reason, a number of effective sensors have been developed for the rapid and highly selective detection of such contaminants. TBA, a well-known aptamer developed to selectively target and thereby inhibit the protein of clinical interest α-thrombin, is receiving increasing attention for sensing applications, particularly for the sensing of different cations. Indeed, TBA, in the presence of these cations, folds into the stable G-quadruplex structure. Furthermore, different cations produce small but significant changes in this structure that result in changes in the electrical responses that TBA can produce. In this article, we give an overview of the expected data regarding the use of TBA in the detection of lead and strontium, calculating the expected electrical response using different measurement techniques. Finally, we conclude that TBA should be able to detect strontium with a sensitivity approximately double that achievable for lead.
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Affiliation(s)
- Eleonora Alfinito
- Dipartimento di Matematica e Fisica 'Ennio De Giorgi', Università del Salento, I-73100 Lecce, Italy
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12
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Andress C, Kappel K, Villena ME, Cuperlovic-Culf M, Yan H, Li Y. DAPTEV: Deep aptamer evolutionary modelling for COVID-19 drug design. PLoS Comput Biol 2023; 19:e1010774. [PMID: 37406007 DOI: 10.1371/journal.pcbi.1010774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/13/2023] [Indexed: 07/07/2023] Open
Abstract
Typical drug discovery and development processes are costly, time consuming and often biased by expert opinion. Aptamers are short, single-stranded oligonucleotides (RNA/DNA) that bind to target proteins and other types of biomolecules. Compared with small-molecule drugs, aptamers can bind to their targets with high affinity (binding strength) and specificity (uniquely interacting with the target only). The conventional development process for aptamers utilizes a manual process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX), which is costly, slow, dependent on library choice and often produces aptamers that are not optimized. To address these challenges, in this research, we create an intelligent approach, named DAPTEV, for generating and evolving aptamer sequences to support aptamer-based drug discovery and development. Using the COVID-19 spike protein as a target, our computational results suggest that DAPTEV is able to produce structurally complex aptamers with strong binding affinities.
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Affiliation(s)
- Cameron Andress
- Department of Computer Science, Brock University, St. Catharines, Canada
| | - Kalli Kappel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | | | - Hongbin Yan
- Department of Chemistry, Brock University, St. Catharines, Canada
| | - Yifeng Li
- Department of Computer Science, Brock University, St. Catharines, Canada
- Department of Biological Sciences, Brock University, St. Catharines, Canada
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13
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Arese M, Mahmoudian M, Bussolino F. RNA aptamer-mediated gene therapy of prostate cancer: lessons from the past and future directions. Expert Opin Drug Deliv 2023; 20:1609-1621. [PMID: 38058168 DOI: 10.1080/17425247.2023.2292691] [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: 09/22/2023] [Accepted: 12/04/2023] [Indexed: 12/08/2023]
Abstract
INTRODUCTION Prostate cancer (PCa) is one of the most prevalent cancers in the world, and the fifth cause of death from cancer in men. Among the non-surgical treatments for PCa, gene therapy strategies are in the early stages of development and recent clinical trials have provided new insights suggesting promising future. AREAS COVERED Recently, the creation of targeted gene delivery systems, based on specific PCa cell surface markers, has been viewed as a viable therapeutic approach. Prostate-specific membrane antigen (PSMA) is vastly expressed in nearly all prostate malignancies, and the intensity of expression increases with tumor aggressiveness, androgen independence, and metastasis. RNA aptamers are short and single-stranded oligonucleotides, which selectively bind to a specific ligand on the surface of the cells, which makes them fascinating small molecules for target delivery of therapeutics. PSMA-selective RNA aptamers represent great potential for developing targeted-gene delivery tools for PCa. EXPERT OPINION This review provides a thorough horizon for the researchers interested in developing targeted gene delivery systems for PCa via PSMA RNA aptamers. In addition, we provided general information about different prospects of RNA aptamers including discovery approaches, stability, safety, and pharmacokinetics.
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Affiliation(s)
- Marco Arese
- Department of Oncology, University of Torino, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Mohammad Mahmoudian
- Department of Oncology, University of Torino, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Federico Bussolino
- Department of Oncology, University of Torino, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
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14
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Aslan Y, Atabay M, Chowdhury HK, Göktürk I, Saylan Y, Inci F. Aptamer-Based Point-of-Care Devices: Emerging Technologies and Integration of Computational Methods. BIOSENSORS 2023; 13:bios13050569. [PMID: 37232930 DOI: 10.3390/bios13050569] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023]
Abstract
Recent innovations in point-of-care (POC) diagnostic technologies have paved a critical road for the improved application of biomedicine through the deployment of accurate and affordable programs into resource-scarce settings. The utilization of antibodies as a bio-recognition element in POC devices is currently limited due to obstacles associated with cost and production, impeding its widespread adoption. One promising alternative, on the other hand, is aptamer integration, i.e., short sequences of single-stranded DNA and RNA structures. The advantageous properties of these molecules are as follows: small molecular size, amenability to chemical modification, low- or nonimmunogenic characteristics, and their reproducibility within a short generation time. The utilization of these aforementioned features is critical in developing sensitive and portable POC systems. Furthermore, the deficiencies related to past experimental efforts to improve biosensor schematics, including the design of biorecognition elements, can be tackled with the integration of computational tools. These complementary tools enable the prediction of the reliability and functionality of the molecular structure of aptamers. In this review, we have overviewed the usage of aptamers in the development of novel and portable POC devices, in addition to highlighting the insights that simulations and other computational methods can provide into the use of aptamer modeling for POC integration.
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Affiliation(s)
- Yusuf Aslan
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Maryam Atabay
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Hussain Kawsar Chowdhury
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Ilgım Göktürk
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Yeşeren Saylan
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Fatih Inci
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
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15
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Selvam R, Lim IHY, Lewis JC, Lim CH, Yap MKK, Tan HS. Selecting antibacterial aptamers against the BamA protein in Pseudomonas aeruginosa by incorporating genetic algorithm to optimise computational screening method. Sci Rep 2023; 13:7582. [PMID: 37164985 PMCID: PMC10170454 DOI: 10.1038/s41598-023-34643-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/04/2023] [Indexed: 05/12/2023] Open
Abstract
Antibiotic resistance is one of the biggest threats to global health resulting in an increasing number of people suffering from severe illnesses or dying due to infections that were once easily curable with antibiotics. Pseudomonas aeruginosa is a major pathogen that has rapidly developed antibiotic resistance and WHO has categorised this pathogen under the critical list. DNA aptamers can act as a potential candidate for novel antimicrobial agents. In this study, we demonstrated that an existing aptamer is able to affect the growth of P. aeruginosa. A computational screen for aptamers that could bind to a well-conserved and essential outer membrane protein, BamA in Gram-negative bacteria was conducted. Molecular docking of about 100 functional DNA aptamers with BamA protein was performed via both local and global docking approaches. Additionally, genetic algorithm analysis was carried out to rank the aptamers based on their binding affinity. The top hits of aptamers with good binding to BamA protein were synthesised to investigate their in vitro antibacterial activity. Among all aptamers, Apt31, which is known to bind to an antitumor, Daunomycin, exhibited the highest HADDOCK score and resulted in a significant (p < 0.05) reduction in P. aeruginosa growth. Apt31 also induced membrane disruption that resulted in DNA leakage. Hence, computational screening may result in the identification of aptamers that bind to the desired active site with high affinity.
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Affiliation(s)
- Rupany Selvam
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Ian Han Yan Lim
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | | | - Chern Hong Lim
- School of Information Technology, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | | | - Hock Siew Tan
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia.
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, Malaysia.
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16
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Zhuo Y, Fu B, Peng R, Ma C, Xie S, Qiu L. Aptamer-based expansion microscopy platform enables signal-amplified imaging of dendritic spines. Talanta 2023; 260:124541. [PMID: 37087946 DOI: 10.1016/j.talanta.2023.124541] [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: 03/07/2023] [Revised: 04/04/2023] [Accepted: 04/08/2023] [Indexed: 04/25/2023]
Abstract
Super-resolution imaging of dendritic spines (DS) can provide valuable information for mechanistic studies related to synaptic physiology and neural plasticity, but challenged by their small dimension (50-200 nm) below the spatial resolution of conventional optical microscopes. In this work, by combining the molecular recognition specificity of aptamer with high programmability of DNA nanotechnology, we developed an expansion microscopy (ExM) platform for imaging DS with enhanced spatial resolution and amplified signal output. Our results demonstrated that the aptamer probe could specifically bind to DS of primary hippocampal neurons. With physical expansion, the DS structure could be effectively enlarged by 4-5 folds, leading to the generation of more structural information. Meantime, the aptamer binding signal could be readily amplified by the introduction of DNA signal amplification strategy, overcoming the drawback of fluorescence dilution during the ExM treatment. This platform enabled evaluation of ischemia-induced early stroke based on the morphological change of DS, highlighting a promising avenue for studying nanoscale structures in biological systems.
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Affiliation(s)
- Yuting Zhuo
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Bo Fu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Ruizi Peng
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Changbei Ma
- School of Life Sciences, Central South University, China
| | - Sitao Xie
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China; Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
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17
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Aptamers targeting SARS-COV-2: a promising tool to fight against COVID-19. Trends Biotechnol 2023; 41:528-544. [PMID: 35995601 PMCID: PMC9340053 DOI: 10.1016/j.tibtech.2022.07.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 12/02/2022]
Abstract
SARS-CoV-2, the causative agent of COVID-19, remains among the main causes of global mortality. Although antigen/antibody-based immunoassays and neutralizing antibodies targeting SARS-CoV-2 have been successfully developed over the past 2 years, they are often inefficient and unreliable for emerging SARS-CoV-2 variants. Novel approaches against SARS-CoV-2 and its variants are therefore urgently needed. Aptamers have been developed for the detection and inhibition of several different viruses such as HIV, influenza viruses, Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV. Aptamers targeting SARS-CoV-2 represent a promising tool in the fight against COVID-19, which is of paramount importance for the current and any future pandemics. This review presents recent advances and future trends in the development of aptamer-based approaches for SARS-CoV-2 diagnosis and treatment.
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18
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Abreu RDS, Antunes D, Moreira ADS, Passetti F, Mendonça JB, de Araújo NS, Sassaro TF, Alberto AVP, Carrossini N, Fernandes PV, Costa MA, Guimarães ACR, Degrave WMS, Waghabi MC. Next Generation of Ovarian Cancer Detection Using Aptamers. Int J Mol Sci 2023; 24:ijms24076315. [PMID: 37047289 PMCID: PMC10094455 DOI: 10.3390/ijms24076315] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 03/30/2023] Open
Abstract
Ovarian cancer is among the seven most common types of cancer in women, being the most fatal gynecological tumor, due to the difficulty of detection in early stages. Aptamers are important tools to improve tumor diagnosis through the recognition of specific molecules produced by tumors. Here, aptamers and their potential targets in ovarian cancer cells were analyzed by in silico approaches. Specific aptamers were selected by the Cell-SELEX method using Caov-3 and OvCar-3 cells. The five most frequent aptamers obtained from the last round of selection were computationally modeled. The potential targets for those aptamers in cells were proposed by analyzing proteomic data available for the Caov-3 and OvCar-3 cell lines. Overexpressed proteins for each cell were characterized as to their three-dimensional model, cell location, and electrostatic potential. As a result, four specific aptamers for ovarian tumors were selected: AptaC2, AptaC4, AptaO1, and AptaO2. Potential targets were identified for each aptamer through Molecular Docking, and the best complexes were AptaC2-FXYD3, AptaC4-ALPP, AptaO1-TSPAN15, and AptaO2-TSPAN15. In addition, AptaC2 and AptaO1 could detect different stages and subtypes of ovarian cancer tissue samples. The application of this technology makes it possible to propose new molecular biomarkers for the differential diagnosis of epithelial ovarian cancer.
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Affiliation(s)
- Rayane da Silva Abreu
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Deborah Antunes
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Aline dos Santos Moreira
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Fabio Passetti
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Curitiba 81350-010, Brazil
| | - Julia Badaró Mendonça
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Natássia Silva de Araújo
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Tayanne Felippe Sassaro
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Anael Viana Pinto Alberto
- Laboratório de Tecnologia de Pós, Instituto Nacional de Tecnologia, Rio de Janeiro 20081-312, Brazil
| | - Nina Carrossini
- Divisão de Patologia (DIPAT), Instituto Nacional do Câncer (INCA), Rio de Janeiro 20220-400, Brazil
| | | | - Mayla Abrahim Costa
- Laboratório de Tecnologia Imunológica, Instituto de Tecnologia em Imunobiológicos, Bio-Manguinhos, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Ana Carolina Ramos Guimarães
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
- Correspondence: (A.C.R.G.); (M.C.W.); Tel.: +55-21-3865-8159 (M.C.W.); Fax: +55-21-2590-3495 (M.C.W.)
| | - Wim Maurits Sylvain Degrave
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Mariana Caldas Waghabi
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
- Correspondence: (A.C.R.G.); (M.C.W.); Tel.: +55-21-3865-8159 (M.C.W.); Fax: +55-21-2590-3495 (M.C.W.)
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19
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Dixit R, Khambhati K, Supraja KV, Singh V, Lederer F, Show PL, Awasthi MK, Sharma A, Jain R. Application of machine learning on understanding biomolecule interactions in cellular machinery. BIORESOURCE TECHNOLOGY 2023; 370:128522. [PMID: 36565819 DOI: 10.1016/j.biortech.2022.128522] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Machine learning (ML) applications have become ubiquitous in all fields of research including protein science and engineering. Apart from protein structure and mutation prediction, scientists are focusing on knowledge gaps with respect to the molecular mechanisms involved in protein binding and interactions with other components in the experimental setups or the human body. Researchers are working on several wet-lab techniques and generating data for a better understanding of concepts and mechanics involved. The information like biomolecular structure, binding affinities, structure fluctuations and movements are enormous which can be handled and analyzed by ML. Therefore, this review highlights the significance of ML in understanding the biomolecular interactions while assisting in various fields of research such as drug discovery, nanomedicine, nanotoxicity and material science. Hence, the way ahead would be to force hand-in hand of laboratory work and computational techniques.
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Affiliation(s)
- Rewati Dixit
- Waste Treatment Laboratory, Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Haus-khas, New Delhi 110016, India
| | - Khushal Khambhati
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana 382715, Gujarat, India
| | - Kolli Venkata Supraja
- Waste Treatment Laboratory, Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Haus-khas, New Delhi 110016, India
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana 382715, Gujarat, India
| | - Franziska Lederer
- Helmholtz-Zentrum Dresden-Rossendorf, Helmholtz Institute Freiberg for Resource Technology, Bautzner landstrasse 400, 01328 Dresden, Germany
| | - Pau-Loke Show
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China; Department of Sustainable Engineering, Saveetha School of Engineering, SIMATS, Chennai 602105, India; Department of Chemical and Environmental Engineering, University of Nottingham, Malaysia, 43500 Semenyih, Selangor Darul Ehsan, Malaysia
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Abhinav Sharma
- Institute Theory of Polymers, Leibniz Institute for Polymer Research, Hohe Strasse 6, 01069 Dresden, Germany
| | - Rohan Jain
- Helmholtz-Zentrum Dresden-Rossendorf, Helmholtz Institute Freiberg for Resource Technology, Bautzner landstrasse 400, 01328 Dresden, Germany.
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20
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Design and Prediction of Aptamers Assisted by In Silico Methods. Biomedicines 2023; 11:biomedicines11020356. [PMID: 36830893 PMCID: PMC9953197 DOI: 10.3390/biomedicines11020356] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
An aptamer is a single-stranded DNA or RNA that binds to a specific target with high binding affinity. Aptamers are developed through the process of systematic evolution of ligands by exponential enrichment (SELEX), which is repeated to increase the binding power and specificity. However, the SELEX process is time-consuming, and the characterization of aptamer candidates selected through it requires additional effort. Here, we describe in silico methods in order to suggest the most efficient way to develop aptamers and minimize the laborious effort required to screen and optimise aptamers. We investigated several methods for the estimation of aptamer-target molecule binding through conformational structure prediction, molecular docking, and molecular dynamic simulation. In addition, examples of machine learning and deep learning technologies used to predict the binding of targets and ligands in the development of new drugs are introduced. This review will be helpful in the development and application of in silico aptamer screening and characterization.
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21
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Perez Tobia J, Huang PJJ, Ding Y, Saran Narayan R, Narayan A, Liu J. Machine Learning Directed Aptamer Search from Conserved Primary Sequences and Secondary Structures. ACS Synth Biol 2023; 12:186-195. [PMID: 36594697 DOI: 10.1021/acssynbio.2c00462] [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] [Indexed: 01/04/2023]
Abstract
Computer-aided prediction of aptamer sequences has been focused on primary sequence alignment and motif comparison. We observed that many aptamers have a conserved hairpin, yet the sequence of the hairpin can be highly variable. Taking such secondary structure information into consideration, a new algorithm combining conserved primary sequences and secondary structures is developed, which combines three scores based on sequence abundance, stability, and structure, respectively. This algorithm was used in the prediction of aptamers from the caffeine and theophylline selections. In the late rounds of the selections, when the libraries were converged, the predicted sequences matched well with the most abundant sequences. When the libraries were far from convergence and the sequences were deemed challenging for traditional analysis methods, this algorithm still predicted aptamer sequences that were experimentally verified by isothermal titration calorimetry. This algorithm paves a new way to look for patterns in aptamer selection libraries and mimics the sequence evolution process. It will help shorten the aptamer selection time and promote the biosensor and chemical biology applications of aptamers.
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Affiliation(s)
- Javier Perez Tobia
- Department of Computer Science, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Yuzhe Ding
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran Narayan
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Apurva Narayan
- Department of Computer Science, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada.,Department of Computer Science, Western University, London, Ontario N6A 3K7, Canada.,Systems Design Engineering, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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22
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Lam SY, Lau HL, Kwok CK. Capture-SELEX: Selection Strategy, Aptamer Identification, and Biosensing Application. BIOSENSORS 2022; 12:bios12121142. [PMID: 36551109 PMCID: PMC9776347 DOI: 10.3390/bios12121142] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 06/01/2023]
Abstract
Small-molecule contaminants, such as antibiotics, pesticides, and plasticizers, have emerged as one of the substances most detrimental to human health and the environment. Therefore, it is crucial to develop low-cost, user-friendly, and portable biosensors capable of rapidly detecting these contaminants. Antibodies have traditionally been used as biorecognition elements. However, aptamers have recently been applied as biorecognition elements in aptamer-based biosensors, also known as aptasensors. The systematic evolution of ligands by exponential enrichment (SELEX) is an in vitro technique used to generate aptamers that bind their targets with high affinity and specificity. Over the past decade, a modified SELEX method known as Capture-SELEX has been widely used to generate DNA or RNA aptamers that bind small molecules. In this review, we summarize the recent strategies used for Capture-SELEX, describe the methods commonly used for detecting and characterizing small-molecule-aptamer interactions, and discuss the development of aptamer-based biosensors for various applications. We also discuss the challenges of the Capture-SELEX platform and biosensor development and the possibilities for their future application.
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Affiliation(s)
- Sin Yu Lam
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China
| | - Hill Lam Lau
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China
| | - Chun Kit Kwok
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
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23
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Sun D, Sun M, Zhang J, Lin X, Zhang Y, Lin F, Zhang P, Yang C, Song J. Computational tools for aptamer identification and optimization. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Hasanzadeh A, Hamblin MR, Kiani J, Noori H, Hardie JM, Karimi M, Shafiee H. Could artificial intelligence revolutionize the development of nanovectors for gene therapy and mRNA vaccines? NANO TODAY 2022; 47:101665. [PMID: 37034382 PMCID: PMC10081506 DOI: 10.1016/j.nantod.2022.101665] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Gene therapy enables the introduction of nucleic acids like DNA and RNA into host cells, and is expected to revolutionize the treatment of a wide range of diseases. This growth has been further accelerated by the discovery of CRISPR/Cas technology, which allows accurate genomic editing in a broad range of cells and organisms in vitro and in vivo. Despite many advances in gene delivery and the development of various viral and non-viral gene delivery vectors, the lack of highly efficient non-viral systems with low cellular toxicity remains a challenge. The application of cutting-edge technologies such as artificial intelligence (AI) has great potential to find new paradigms to solve this issue. Herein, we review AI and its major subfields including machine learning (ML), neural networks (NNs), expert systems, deep learning (DL), computer vision and robotics. We discuss the potential of AI-based models and algorithms in the design of targeted gene delivery vehicles capable of crossing extracellular and intracellular barriers by viral mimicry strategies. We finally discuss the role of AI in improving the function of CRISPR/Cas systems, developing novel nanobots, and mRNA vaccine carriers.
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Affiliation(s)
- Akbar Hasanzadeh
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa
- Radiation Biology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Jafar Kiani
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Noori
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Joseph M. Hardie
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02139 USA
| | - Mahdi Karimi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Research Center for Science and Technology in Medicine, Tehran University of Medical Sciences, Tehran 141556559, Iran
- Applied Biotechnology Research Centre, Tehran Medical Science, Islamic Azad University, Tehran 1584743311, Iran
| | - Hadi Shafiee
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02139 USA
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Amundarain A, Pastor F, Prósper F, Agirre X. Aptamers, a New Therapeutic Opportunity for the Treatment of Multiple Myeloma. Cancers (Basel) 2022; 14:5471. [PMID: 36358889 PMCID: PMC9657029 DOI: 10.3390/cancers14215471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/31/2022] [Accepted: 11/04/2022] [Indexed: 08/30/2023] Open
Abstract
Multiple Myeloma (MM) remains an incurable disease due to high relapse rates and fast development of drug resistances. The introduction of monoclonal antibodies (mAb) has caused a paradigm shift in MM treatment, paving the way for targeted approaches with increased efficacy and reduced toxicities. Nevertheless, antibody-based therapies face several difficulties such as high immunogenicity, high production costs and limited conjugation capacity, which we believe could be overcome by the introduction of nucleic acid aptamers. Similar to antibodies, aptamers can bind to their targets with great affinity and specificity. However, their chemical nature reduces their immunogenicity and production costs, while it enables their conjugation to a wide variety of cargoes for their use as delivery agents. In this review, we summarize several aptamers that have been tested against MM specific targets with promising results, establishing the rationale for the further development of aptamer-based strategies against MM. In this direction, we believe that the study of novel plasma cell surface markers, the development of intracellular aptamers and further research on aptamers as building blocks for complex nanomedicines will lead to the generation of next-generation targeted approaches that will undoubtedly contribute to improve the management and life quality of MM patients.
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Affiliation(s)
- Ane Amundarain
- Center for Applied Medical Research (CIMA), IDISNA, University of Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 31008 Pamplona, Spain
| | - Fernando Pastor
- Center for Applied Medical Research (CIMA), IDISNA, University of Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 31008 Pamplona, Spain
| | - Felipe Prósper
- Center for Applied Medical Research (CIMA), IDISNA, University of Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 31008 Pamplona, Spain
- Hematology Department, Clínica Universidad de Navarra, CCUN, University of Navarra, 31008 Pamplona, Spain
| | - Xabier Agirre
- Center for Applied Medical Research (CIMA), IDISNA, University of Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 31008 Pamplona, Spain
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26
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Yunussova N, Sypabekova M, Zhumabekova Z, Matkarimov B, Kanayeva D. A Novel ssDNA Aptamer Targeting Carcinoembryonic Antigen: Selection and Characterization. BIOLOGY 2022; 11:biology11101540. [PMID: 36290442 PMCID: PMC9598387 DOI: 10.3390/biology11101540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/20/2022]
Abstract
One of the major causes of a drastically shorter life expectancy and one of the most prevalent diseases in the world today is cancer. Given the data on the rise in cancer cases throughout the world, it is obvious that, despite the diagnostic techniques currently being used, there is a pressing need to develop precise and sensitive techniques for early diagnosis of the disease. A high degree of affinity and specificity towards particular targets is maintained by the short nucleic acid molecules known as aptamers. Aptamers outperform antibodies due to their unique benefits, such as their simplicity in synthesis and modification, lack of toxicity, and long-term stability. Utilizing an accurate recognition element and a robust signal transduction mechanism, molecular diagnostics can be extremely sensitive and specific. In this study, development of new single-stranded DNA aptamers against CEA for use in cancer diagnostics was accomplished using SELEX and NGS methods. As a result of 12 iterative SELEX rounds, nine aptamer candidates against CEA were developed. NGS comparative analysis revealed that round twelve had an enriched number of aptamers that were specifically bound, as opposed to round eight. Among the selected nine sequences characterized by bioinformatics analysis and ELONA, an aptamer sequence with the highest specificity and affinity for the target protein was identified and further examined. Aptamer sequence (6) was screened in a concentration-dependent assay, specificity analysis was performed, and its potential secondary and tertiary structures were predicted, which enabled us to test one of the possible putative interactions with CEA. Finally, aptamer sequence (6) labelled with a Cy5 fluorescent tag was used in confocal microscopy to observe its binding towards the CEA expressed in HT-29 human colon adenocarcinoma cell line.
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Affiliation(s)
- Nigara Yunussova
- Ph.D. Program in Life Sciences, Nazarbayev University, 53 Kabanbay Batyr Ave., Astana 010000, Kazakhstan
| | - Marzhan Sypabekova
- National Laboratory Astana, Nazarbayev University, 53 Kabanbay Batyr Ave., Astana 010000, Kazakhstan
| | - Zhazira Zhumabekova
- M.Sc. Program in Biological Sciences, Nazarbayev University, 53 Kabanbay Batyr Ave., Astana 010000, Kazakhstan
| | - Bakhyt Matkarimov
- National Laboratory Astana, Nazarbayev University, 53 Kabanbay Batyr Ave., Astana 010000, Kazakhstan
| | - Damira Kanayeva
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, 53 Kabanbay Batyr Ave., Astana 010000, Kazakhstan
- Correspondence:
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27
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Liu Z, Xue J, Chen L, Ma L, Yang H, Zhang Y, Miao M. A signal-off aptamer sensor based on competition with complementary DNA and click polymerization for electrochemical detection of AFB1. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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28
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Douaki A, Garoli D, Inam AKMS, Angeli MAC, Cantarella G, Rocchia W, Wang J, Petti L, Lugli P. Smart Approach for the Design of Highly Selective Aptamer-Based Biosensors. BIOSENSORS 2022; 12:bios12080574. [PMID: 36004970 PMCID: PMC9405846 DOI: 10.3390/bios12080574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022]
Abstract
Aptamers are chemically synthesized single-stranded DNA or RNA oligonucleotides widely used nowadays in sensors and nanoscale devices as highly sensitive biorecognition elements. With proper design, aptamers are able to bind to a specific target molecule with high selectivity. To date, the systematic evolution of ligands by exponential enrichment (SELEX) process is employed to isolate aptamers. Nevertheless, this method requires complex and time-consuming procedures. In silico methods comprising machine learning models have been recently proposed to reduce the time and cost of aptamer design. In this work, we present a new in silico approach allowing the generation of highly sensitive and selective RNA aptamers towards a specific target, here represented by ammonium dissolved in water. By using machine learning and bioinformatics tools, a rational design of aptamers is demonstrated. This “smart” SELEX method is experimentally proved by choosing the best five aptamer candidates obtained from the design process and applying them as functional elements in an electrochemical sensor to detect, as the target molecule, ammonium at different concentrations. We observed that the use of five different aptamers leads to a significant difference in the sensor’s response. This can be explained by considering the aptamers’ conformational change due to their interaction with the target molecule. We studied these conformational changes using a molecular dynamics simulation and suggested a possible explanation of the experimental observations. Finally, electrochemical measurements exposing the same sensors to different molecules were used to confirm the high selectivity of the designed aptamers. The proposed in silico SELEX approach can potentially reduce the cost and the time needed to identify the aptamers and potentially be applied to any target molecule.
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Affiliation(s)
- Ali Douaki
- Faculty of Science and Technology, Libera Università di Bolzano, Piazza Università 1, 39100 Bolzano, Italy; (A.K.M.S.I.); (M.A.C.A.); (G.C.); (L.P.)
- Correspondence: (A.D.); (P.L.)
| | - Denis Garoli
- Istituto Italiano di Tecnologia, Via Morego, 30, 16163 Genova, Italy;
| | - A. K. M. Sarwar Inam
- Faculty of Science and Technology, Libera Università di Bolzano, Piazza Università 1, 39100 Bolzano, Italy; (A.K.M.S.I.); (M.A.C.A.); (G.C.); (L.P.)
| | - Martina Aurora Costa Angeli
- Faculty of Science and Technology, Libera Università di Bolzano, Piazza Università 1, 39100 Bolzano, Italy; (A.K.M.S.I.); (M.A.C.A.); (G.C.); (L.P.)
| | - Giuseppe Cantarella
- Faculty of Science and Technology, Libera Università di Bolzano, Piazza Università 1, 39100 Bolzano, Italy; (A.K.M.S.I.); (M.A.C.A.); (G.C.); (L.P.)
| | - Walter Rocchia
- CONCEPT Lab, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genova, Italy;
| | - Jiahai Wang
- School of Mechanical and Electrical Engineering, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China;
| | - Luisa Petti
- Faculty of Science and Technology, Libera Università di Bolzano, Piazza Università 1, 39100 Bolzano, Italy; (A.K.M.S.I.); (M.A.C.A.); (G.C.); (L.P.)
| | - Paolo Lugli
- Faculty of Science and Technology, Libera Università di Bolzano, Piazza Università 1, 39100 Bolzano, Italy; (A.K.M.S.I.); (M.A.C.A.); (G.C.); (L.P.)
- Correspondence: (A.D.); (P.L.)
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Nucleic Acid Aptamers Emerging as Modulators of G-Protein-Coupled Receptors: Challenge to Difficult Cell Surface Proteins. Cells 2022; 11:cells11111825. [PMID: 35681520 PMCID: PMC9180700 DOI: 10.3390/cells11111825] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 05/29/2022] [Accepted: 05/31/2022] [Indexed: 02/04/2023] Open
Abstract
G-protein-coupled receptors (GPCRs), among various cell surface proteins, are essential targets in the fields of basic science and drug discovery. The discovery and development of modulators for the receptors have provided deep insights into the mechanism of action of receptors and have led to a new therapeutic option for human diseases. Although various modulators against GPCRs have been developed to date, the identification of new modulators for GPCRs remains a challenge due to several technical problems and limitations. To overcome this situation, a variety of strategies have been developed by several modalities, including nucleic acid aptamers, which are emerging as unique molecules isolated by a repetitive selection process against various types of targets from an enormous combinatorial library. This review summarized the achievements in the development of aptamers targeting GPCRs, and discussed their isolation methods and the diverse functional features of aptamers against GPCRs.
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30
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Aptamers: Functional-Structural Studies and Biomedical Applications. Int J Mol Sci 2022; 23:ijms23094796. [PMID: 35563186 PMCID: PMC9101710 DOI: 10.3390/ijms23094796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 04/24/2022] [Indexed: 11/26/2022] Open
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31
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Jiang H, Zhang Z, Yu Y, Chu HY, Yu S, Yao S, Zhang G, Zhang BT. Drug Discovery of DKK1 Inhibitors. Front Pharmacol 2022; 13:847387. [PMID: 35355709 PMCID: PMC8959454 DOI: 10.3389/fphar.2022.847387] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 02/21/2022] [Indexed: 12/24/2022] Open
Abstract
Dickkopf-1 (DKK1) is a well-characterized Wnt inhibitor and component of the Wnt/β-catenin signaling pathway, whose dysregulation is associated with multiple abnormal pathologies including osteoporosis, Alzheimer's disease, diabetes, and various cancers. The Wnt signaling pathway has fundamental roles in cell fate determination, cell proliferation, and survival; thus, its mis-regulation can lead to disease. Although DKK1 is involved in other signaling pathways, including the β-catenin-independent Wnt pathway and the DKK1/CKAP4 pathway, the inhibition of DKK1 to propagate Wnt/β-catenin signals has been validated as an effective way to treat related diseases. In fact, strategies for developing DKK1 inhibitors have produced encouraging clinical results in different pathological models, and many publications provide detailed information about these inhibitors, which include small molecules, antibodies, and nucleic acids, and may function at the protein or mRNA level. However, no systematic review has yet provided an overview of the various aspects of their development and prospects. Therefore, we review the DKK1 inhibitors currently available or under study and provide an outlook on future studies involving DKK1 and drug discovery.
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Affiliation(s)
- Hewen Jiang
- School of Chinese Medicine, Chinese University of Hong Kong, Hong Kong, China.,Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, China
| | - Zongkang Zhang
- School of Chinese Medicine, Chinese University of Hong Kong, Hong Kong, China.,Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, China
| | - Yuanyuan Yu
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, China.,Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.,Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Hang Yin Chu
- School of Chinese Medicine, Chinese University of Hong Kong, Hong Kong, China.,Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, China
| | - Sifan Yu
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, China.,Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.,Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Shanshan Yao
- School of Chinese Medicine, Chinese University of Hong Kong, Hong Kong, China.,Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, China
| | - Ge Zhang
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, China.,Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.,Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Bao-Ting Zhang
- School of Chinese Medicine, Chinese University of Hong Kong, Hong Kong, China.,Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, China
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32
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Nosrati M, Roushani M. Three-dimensional modeling of streptomycin binding single-stranded DNA for aptamer-based biosensors, a molecular dynamics simulation approach. J Biomol Struct Dyn 2022; 41:3430-3439. [PMID: 35297324 DOI: 10.1080/07391102.2022.2050945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Streptomycin (STR) an aminoglycoside antibiotic which is used against bacteria in human and animal infection, have serious side effects on different parts of human body. Therefore, there is a crucial need to detect trace amount of it in serum and food products. Aptamers are oligonucleotides or peptides, which bind their targets with high affinity and specificity. These properties make aptamers as suitable candidates for biosensing applications. A 79-mer ss-DNA aptamer was applied for the detection of small amount of STR in various aptasensors. But there is no structural information on the STR-binding aptamer and molecular details underlying the aptamer-STR binding remain unexplored. In this study we provided a 3D-structural model for 79-mer ss-DNA aptamer from the sequence. Using docking program and molecular dynamics (MD) simulation we predicted the binding pocket of ss-DNA aptamer. Our results show STR streptose ring is buried within the groove of DNA model and capped by non Watson-Crick bases. STR interacts with aptamer through forming stable hydrogen bonds. Our computational findings are in fair agreement with experimental results. With the atomic structural details, we gained new insight into the Apt-STR binding interaction that can help to further optimize aptamer efficiency in biosensing applications.Communicated by Ramaswamy H. Sarma.
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Bilibana MP, Citartan M, Fuku X, Jijana AN, Mathumba P, Iwuoha E. Aptamers functionalized hybrid nanomaterials for algal toxins detection and decontamination in aquatic system: Current progress, opportunities, and challenges. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 232:113249. [PMID: 35104779 DOI: 10.1016/j.ecoenv.2022.113249] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Purification and detection of algal toxins is the most effective technique to ensure that people have clean and safe drinking water. To achieve these objectives, various state-of-the-art technologies were designed and fabricated to decontaminate and detect algal toxins in aquatic environments. Amongst these technologies, aptamer-functionalized hybrid nanomaterials conjugates have received significant consideration as a result of their several benefits over other methods, such as good controllable selectivity, low immunogenicity, and biocompatibility. Because of their excellent properties, aptamer-functionalized hybrid nanomaterials conjugates are one of several remarkable agents. Several isolated aptamer sequences for algal toxins are addressed in this review, as well as aptasensor and decontamination aptamer functionalized metal nanoparticle-derived hybrid nanocomposites applications. In addition, we present diverse aptamer-functionalized hybrid nanomaterial conjugates designs and their applications for sensing and decontamination.
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Affiliation(s)
- Mawethu Pascoe Bilibana
- Department of Chemistry, School of Physical and Chemical Sciences, Faculty of Natural and Agricultural Sciences, Mafikeng Campus, North-West University, Private Bag X2046, Mmabatho 2735, South Africa; Material Science Innovation and Modelling (MaSIM) Research Focus Area, Faculty of Natural and Agricultural Sciences, Mafikeng Campus, North-West University, Private Bag X2046, Mmabatho 2735, South Africa.
| | - Marimuthu Citartan
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas 13200, Pulau Pinang, Malaysia
| | - Xolile Fuku
- Institute for Nanotechnology and Water Sustainability (iNanoWS), Florida Campus, College of Science, Engineering and Technology, University of South Africa, Johannesburg 1710, South Africa
| | - Abongile Nwabisa Jijana
- National Innovation Centre, Advanced Material Division, Mintek, 200 Malibongwe Drive, Private Bag x 3015, Johannesburg, Gauteng, South Africa
| | - Penny Mathumba
- National Innovation Centre, Advanced Material Division, Mintek, 200 Malibongwe Drive, Private Bag x 3015, Johannesburg, Gauteng, South Africa
| | - Emmanuel Iwuoha
- SensorLab (University of Western Cape Sensor Laboratories), Chemical Sciences Building, University of the Western Cape, Bellville, 7535 Cape Town, South Africa
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34
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Qi S, Duan N, Khan IM, Dong X, Zhang Y, Wu S, Wang Z. Strategies to manipulate the performance of aptamers in SELEX, post-SELEX and microenvironment. Biotechnol Adv 2022; 55:107902. [DOI: 10.1016/j.biotechadv.2021.107902] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/21/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023]
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35
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Murakami K, Izuo N, Bitan G. Aptamers targeting amyloidogenic proteins and their emerging role in neurodegenerative diseases. J Biol Chem 2022; 298:101478. [PMID: 34896392 PMCID: PMC8728582 DOI: 10.1016/j.jbc.2021.101478] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/24/2021] [Accepted: 12/02/2021] [Indexed: 01/08/2023] Open
Abstract
Aptamers are oligonucleotides selected from large pools of random sequences based on their affinity for bioactive molecules and are used in similar ways to antibodies. Aptamers provide several advantages over antibodies, including their small size, facile, large-scale chemical synthesis, high stability, and low immunogenicity. Amyloidogenic proteins, whose aggregation is relevant to neurodegenerative diseases, such as Alzheimer's, Parkinson's, and prion diseases, are among the most challenging targets for aptamer development due to their conformational instability and heterogeneity, the same characteristics that make drug development against amyloidogenic proteins difficult. Recently, chemical tethering of aptagens (equivalent to antigens) and advances in high-throughput sequencing-based analysis have been used to overcome some of these challenges. In addition, internalization technologies using fusion to cellular receptors and extracellular vesicles have facilitated central nervous system (CNS) aptamer delivery. In view of the development of these techniques and resources, here we review antiamyloid aptamers, highlighting preclinical application to CNS therapy.
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Affiliation(s)
- Kazuma Murakami
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
| | - Naotaka Izuo
- Laboratory of Pharmaceutical Therapy and Neuropharmacology, Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, Brain Research Institute, and Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, USA.
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36
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Chen XF, Zhao X, Yang Z. Aptamer-Based Antibacterial and Antiviral Therapy against Infectious Diseases. J Med Chem 2021; 64:17601-17626. [PMID: 34854680 DOI: 10.1021/acs.jmedchem.1c01567] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA molecules selected in vitro that can bind to a broad range of targets with high affinity and specificity. As promising alternatives to conventional anti-infective agents, aptamers have gradually revealed their potential in the combat against infectious diseases. This article provides an overview on the state-of-art of aptamer-based antibacterial and antiviral therapeutic strategies. Diverse aptamers targeting pathogen-related components or whole pathogenic cells are summarized according to the species of microorganisms. These aptamers exhibited remarkable in vitro and/or in vivo inhibitory effect for pathogenic invasion, enzymatic activities, or viral replication, even for some highly drug-resistant strains and biofilms. Aptamer-mediated drug delivery and controlled drug release strategies are also included herein. Critical technical barriers of therapeutic aptamers are briefly discussed, followed by some future perspectives for their implementation into clinical utility.
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Affiliation(s)
- Xiao-Fei Chen
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou 510070, PR China
| | - Xin Zhao
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou 510070, PR China
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, PR China.,Guangzhou Laboratory, Guangzhou 510320, PR China.,Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, Guangzhou 510005, PR China
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37
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Pheno-SELEX: Engineering Anti-Metastatic Aptamers through Targeting the Invasive Phenotype Using Systemic Evolution of Ligands by Exponential Enrichment. Bioengineering (Basel) 2021; 8:bioengineering8120212. [PMID: 34940365 PMCID: PMC8698736 DOI: 10.3390/bioengineering8120212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 11/24/2022] Open
Abstract
Multiple methods (e.g., small molecules and antibodies) have been engineered to target specific proteins and signaling pathways in cancer. However, many mediators of the cancer phenotype are unknown and the ability to target these phenotypes would help mitigate cancer. Aptamers are small DNA or RNA molecules that are designed for therapeutic use. The design of aptamers to target cancers can be challenging. Accordingly, to engineer functionally anti-metastatic aptamers we used a modification of systemic evolution of ligands by exponential enrichment (SELEX) we call Pheno-SELEX to target a known phenotype of cancer metastasis, i.e., invasion. A highly invasive prostate cancer (PCa) cell line was established and used to identify aptamers that bound to it with high affinity as opposed to a less invasive variant to the cell line. The anti-invasive aptamer (AIA1) was found to inhibit in vitro invasion of the original highly invasive PCa cell line, as well as an additional PCa cell line and an osteosarcoma cell line. AIA1 also inhibited in vivo development of metastasis in both a PCa and osteosarcoma model of metastasis. These results indicate that Pheno-SELEX can be successfully used to identify aptamers without knowledge of underlying molecular targets. This study establishes a new paradigm for the identification of functional aptamers.
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38
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Structural Biology for the Molecular Insight between Aptamers and Target Proteins. Int J Mol Sci 2021; 22:ijms22084093. [PMID: 33920991 PMCID: PMC8071422 DOI: 10.3390/ijms22084093] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers are promising therapeutic and diagnostic agents for various diseases due to their high affinity and specificity against target proteins. Structural determination in combination with multiple biochemical and biophysical methods could help to explore the interacting mechanism between aptamers and their targets. Regrettably, structural studies for aptamer–target interactions are still the bottleneck in this field, which are facing various difficulties. In this review, we first reviewed the methods for resolving structures of aptamer–protein complexes and for analyzing the interactions between aptamers and target proteins. We summarized the general features of the interacting nucleotides and residues involved in the interactions between aptamers and proteins. Challenges and perspectives in current methodologies were discussed. Approaches for determining the binding affinity between aptamers and target proteins as well as modification strategies for stabilizing the binding affinity of aptamers to target proteins were also reviewed. The review could help to understand how aptamers interact with their targets and how alterations such as chemical modifications in the structures affect the affinity and function of aptamers, which could facilitate the optimization and translation of aptamers-based theranostics.
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