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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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2
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Umezawa K, Ikeda R, Sakamoto T, Enomoto Y, Nihashi Y, Shinji S, Shimosato T, Kagami H, Takaya T. Development of the 12-Base Short Dimeric Myogenetic Oligodeoxynucleotide That Induces Myogenic Differentiation. BIOTECH 2024; 13:11. [PMID: 38804293 PMCID: PMC11130974 DOI: 10.3390/biotech13020011] [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: 03/17/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
A myogenetic oligodeoxynucleotide (myoDN), iSN04 (5'-AGA TTA GGG TGA GGG TGA-3'), is a single-stranded 18-base telomeric DNA that serves as an anti-nucleolin aptamer and induces myogenic differentiation, which is expected to be a nucleic acid drug for the prevention of disease-associated muscle wasting. To improve the drug efficacy and synthesis cost of myoDN, shortening the sequence while maintaining its structure-based function is a major challenge. Here, we report the novel 12-base non-telomeric myoDN, iMyo01 (5'-TTG GGT GGG GAA-3'), which has comparable myogenic activity to iSN04. iMyo01 as well as iSN04 promoted myotube formation of primary-cultured human myoblasts with upregulation of myogenic gene expression. Both iMyo01 and iSN04 interacted with nucleolin, but iMyo01 did not bind to berberine, the isoquinoline alkaloid that stabilizes iSN04. Nuclear magnetic resonance revealed that iMyo01 forms a G-quadruplex structure despite its short sequence. Native polyacrylamide gel electrophoresis and a computational molecular dynamics simulation indicated that iMyo01 forms a homodimer to generate a G-quadruplex. These results provide new insights into the aptamer truncation technology that preserves aptamer conformation and bioactivity for the development of efficient nucleic acid drugs.
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Affiliation(s)
- Koji Umezawa
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan; (K.U.); (Y.E.); (T.S.); (H.K.)
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
| | - Rena Ikeda
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
| | - Taiichi Sakamoto
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi 275-0016, Japan;
| | - Yuya Enomoto
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan; (K.U.); (Y.E.); (T.S.); (H.K.)
| | - Yuma Nihashi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Centoral 5-41, 1-1-1 Higashi, Tsukuba 305-8565, Japan;
| | - Sayaka Shinji
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
| | - Takeshi Shimosato
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan; (K.U.); (Y.E.); (T.S.); (H.K.)
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
| | - Hiroshi Kagami
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan; (K.U.); (Y.E.); (T.S.); (H.K.)
| | - Tomohide Takaya
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan; (K.U.); (Y.E.); (T.S.); (H.K.)
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina 399-4598, Japan
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3
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Shin I, Kang K, Kim J, Sel S, Choi J, Lee JW, Kang HY, Song G. AptaTrans: a deep neural network for predicting aptamer-protein interaction using pretrained encoders. BMC Bioinformatics 2023; 24:447. [PMID: 38012571 PMCID: PMC10680337 DOI: 10.1186/s12859-023-05577-6] [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: 08/24/2023] [Accepted: 11/21/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Aptamers, which are biomaterials comprised of single-stranded DNA/RNA that form tertiary structures, have significant potential as next-generation materials, particularly for drug discovery. The systematic evolution of ligands by exponential enrichment (SELEX) method is a critical in vitro technique employed to identify aptamers that bind specifically to target proteins. While advanced SELEX-based methods such as Cell- and HT-SELEX are available, they often encounter issues such as extended time consumption and suboptimal accuracy. Several In silico aptamer discovery methods have been proposed to address these challenges. These methods are specifically designed to predict aptamer-protein interaction (API) using benchmark datasets. However, these methods often fail to consider the physicochemical interactions between aptamers and proteins within tertiary structures. RESULTS In this study, we propose AptaTrans, a pipeline for predicting API using deep learning techniques. AptaTrans uses transformer-based encoders to handle aptamer and protein sequences at the monomer level. Furthermore, pretrained encoders are utilized for the structural representation. After validation with a benchmark dataset, AptaTrans has been integrated into a comprehensive toolset. This pipeline synergistically combines with Apta-MCTS, a generative algorithm for recommending aptamer candidates. CONCLUSION The results show that AptaTrans outperforms existing models for predicting API, and the efficacy of the AptaTrans pipeline has been confirmed through various experimental tools. We expect AptaTrans will enhance the cost-effectiveness and efficiency of SELEX in drug discovery. The source code and benchmark dataset for AptaTrans are available at https://github.com/pnumlb/AptaTrans .
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Affiliation(s)
- Incheol Shin
- Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea
| | - Keumseok Kang
- Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea
| | - Juseong Kim
- Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea
| | - Sanghun Sel
- Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea
| | - Jeonghoon Choi
- Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea
| | - Jae-Wook Lee
- Research & Development, NuclixBio, Seoul, Republic of Korea
| | - Ho Young Kang
- Research & Development, NuclixBio, Seoul, Republic of Korea
| | - Giltae Song
- Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea.
- School of Computer Science and Engineering, Pusan National University, Busan, Republic of Korea.
- Center for Artificial Intelligence Research, Pusan National University, Busan, Republic of Korea.
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4
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Ji C, Wei J, Zhang L, Hou X, Tan J, Yuan Q, Tan W. Aptamer-Protein Interactions: From Regulation to Biomolecular Detection. Chem Rev 2023; 123:12471-12506. [PMID: 37931070 DOI: 10.1021/acs.chemrev.3c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.
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Affiliation(s)
- Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xinru Hou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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5
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Han R, Yoon H, Kim G, Lee H, Lee Y. Revolutionizing Medicinal Chemistry: The Application of Artificial Intelligence (AI) in Early Drug Discovery. Pharmaceuticals (Basel) 2023; 16:1259. [PMID: 37765069 PMCID: PMC10537003 DOI: 10.3390/ph16091259] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/24/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Artificial intelligence (AI) has permeated various sectors, including the pharmaceutical industry and research, where it has been utilized to efficiently identify new chemical entities with desirable properties. The application of AI algorithms to drug discovery presents both remarkable opportunities and challenges. This review article focuses on the transformative role of AI in medicinal chemistry. We delve into the applications of machine learning and deep learning techniques in drug screening and design, discussing their potential to expedite the early drug discovery process. In particular, we provide a comprehensive overview of the use of AI algorithms in predicting protein structures, drug-target interactions, and molecular properties such as drug toxicity. While AI has accelerated the drug discovery process, data quality issues and technological constraints remain challenges. Nonetheless, new relationships and methods have been unveiled, demonstrating AI's expanding potential in predicting and understanding drug interactions and properties. For its full potential to be realized, interdisciplinary collaboration is essential. This review underscores AI's growing influence on the future trajectory of medicinal chemistry and stresses the importance of ongoing synergies between computational and domain experts.
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Affiliation(s)
| | | | | | | | - Yoonji Lee
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
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6
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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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7
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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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8
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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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9
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Nohira N, Shinji S, Nakamura S, Nihashi Y, Shimosato T, Takaya T. Myogenetic Oligodeoxynucleotides as Anti-Nucleolin Aptamers Inhibit the Growth of Embryonal Rhabdomyosarcoma Cells. Biomedicines 2022; 10:2691. [PMID: 36359210 PMCID: PMC9687923 DOI: 10.3390/biomedicines10112691] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 09/29/2023] Open
Abstract
Embryonal rhabdomyosarcoma (ERMS) is the muscle-derived tumor retaining myogenic ability. iSN04 and AS1411, which are myogenetic oligodeoxynucleotides (myoDNs) serving as anti-nucleolin aptamers, have been reported to inhibit the proliferation and induce the differentiation of myoblasts. The present study investigated the effects of iSN04 and AS1411 in vitro on the growth of multiple patient-derived ERMS cell lines, ERMS1, KYM1, and RD. RT-PCR and immunostaining revealed that nucleolin was abundantly expressed and localized in nucleoplasm and nucleoli in all ERMS cell lines, similar to myoblasts. Both iSN04 and AS1411 at final concentrations of 10-30 μM significantly decreased the number of all ERMS cells; however, their optimal conditions were different among the cell lines. In all ERMS cell lines, iSN04 at a final concentration of 10 μM markedly reduced the ratio of EdU+ cells, indicating the inhibition of cell proliferation. Quantitative RT-PCR or immunostaining of phosphorylated histone H3 and myosin heavy chain demonstrated that iSN04 suppressed the cell cycle and partially promoted myogenesis but did not induce apoptosis in ERMS cells. Finally, both iSN04 and AS1411 at final concentrations of 10-30 μM disrupted the formation and outgrowth of RD tumorspheres in three-dimensional culture mimicking in vivo tumorigenesis. In conclusion, ERMS cells expressed nucleolin, and their growth was inhibited by the anti-nucleolin aptamers, iSN04 and AS1411, which modulates several cell cycle-related and myogenic gene expression. The present study provides evidence that anti-nucleolin aptamers can be used as nucleic acid drugs for chemotherapy against ERMS.
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Affiliation(s)
- Naoki Nohira
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Sayaka Shinji
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Shunichi Nakamura
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Yuma Nihashi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Central 5-41, 1-1-1 Higashi, Tsukuba 305-8565, Japan
| | - Takeshi Shimosato
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Tomohide Takaya
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
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10
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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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Novel Design of RNA Aptamers as Cancer Inhibitors and Diagnosis Targeting the Tyrosine Kinase Domain of the NT-3 Growth Factor Receptor Using a Computational Sequence-Based Approach. Molecules 2022; 27:molecules27144518. [PMID: 35889390 PMCID: PMC9320020 DOI: 10.3390/molecules27144518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 12/10/2022] Open
Abstract
Aptamers, the nucleic acid analogs of antibodies, bind to their target molecules with remarkable specificity and sensitivity, making them promising diagnostic and therapeutic tools. The systematic evolution of ligands by exponential enrichment (SELEX) is time-consuming and expensive. However, regardless of those issues, it is the most used in vitro method for selecting aptamers. Therefore, recent studies have used computational approaches to reduce the time and cost associated with the synthesis and selection of aptamers. In an effort to present the potential of computational techniques in aptamer selection, a simple sequence-based method was used to design a 69-nucleotide long aptamer (mod_09) with a relatively stable structure (with a minimum free energy of −32.2 kcal/mol) and investigate its binding properties to the tyrosine kinase domain of the NT-3 growth factor receptor, for the first time, by employing computational modeling and docking tools.
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