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Akmal Shukri AM, Wang SM, Feng C, Chia SL, Mohd Nawi SFA, Citartan M. In silico selection of aptamers against SARS-CoV-2. Analyst 2024. [PMID: 39221970 DOI: 10.1039/d4an00812j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Aptamers are molecular recognition elements that have been extensively deployed in a wide array of applications ranging from diagnostics to therapeutics. Due to their unique properties as compared to antibodies, aptamers were also largely isolated during the COVID-19 pandemic for multiple purposes. Typically generated by conventional SELEX, the inherent drawbacks of the process including the time-consuming, cumbersome and resource-intensive nature catalysed the move to adopt in silico approaches to isolate aptamers. Impressive performances of these in silico-derived aptamers in their respective assays have been documented thus far, bearing testimony to the huge potential of the in silico approaches, akin to the traditional SELEX in isolating aptamers. In this study, we provide an overview of the in silico selection of aptamers against SARS-CoV-2 by providing insights into the basic steps involved, which comprise the selection of the initial single-stranded nucleic acids, determination of the secondary and tertiary structures and in silico approaches that include both rigid docking and molecular dynamics simulations. The different approaches involving aptamers against SARS-CoV-2 were illuminated and the need to verify these aptamers by experimental validation was also emphasized. Cognizant of the need to continuously improve aptamers, the strategies embraced thus far for post-in silico selection modifications were enumerated. Shedding light on the steps involved in the in silico selection can set the stage for further improvisation to augment the functionalities of the aptamers in the future.
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Affiliation(s)
- Amir Muhaimin Akmal Shukri
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia.
- Institute of Medical Molecular Biotechnology (IMMB), Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Seok Mui Wang
- Institute of Medical Molecular Biotechnology (IMMB), Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia.
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
- Non-Destructive Biomedical and Pharmaceutical Research Center, Smart Manufacturing Research Institute (SMRI), Universiti Teknologi MARA, Puncak Alam Campus, Selangor, Malaysia
| | - Chaoli Feng
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia.
| | - Suet Lin Chia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
- UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang, Selangor, Malaysia
| | - Siti Farah Alwani Mohd Nawi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia.
| | - Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia.
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Solanki K, Ahmed N, Srivastava N, Meher N. Prostate-Specific Membrane Antigen-Targeted NIR Phototheranostics for Prostate Cancer. ACS APPLIED BIO MATERIALS 2024. [PMID: 39192748 DOI: 10.1021/acsabm.4c00819] [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: 08/29/2024]
Abstract
The evolution of targeted cancer theranostics has revolutionized personalized medicine by integrating diagnostic and therapeutic capabilities. Prostate-specific membrane antigen (PSMA) has emerged as a key theranostic target in the context of prostate cancer, paving the way for the clinical approval of multiple drugs. However, the persistent challenge of off-target toxicity, which plagues both conventional and advanced treatment modalities such as targeted chemotherapy and radiotherapy, thus demands further innovation. Considering this critical issue, this review discusses the recent advances in the binary treatment techniques, i.e., phototherapies, that have the potential to circumvent the key concern of off-target toxicity associated with personalized chemotherapy and radiotherapy. Precisely, an up-to-date overview of the latest developments in the near-infrared (NIR)-based phototheranostic strategies for prostate cancer by targeting PSMA has been presented. Furthermore, we have discussed the associated particulars that require specific attention in enhancing the translational potential of phototheranostic techniques.
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Affiliation(s)
- Krishna Solanki
- National Institute of Pharmaceutical Education and Research, Raebareli, Lucknow, Uttar Pradesh 226002, India
| | - Nazeer Ahmed
- National Institute of Pharmaceutical Education and Research, Raebareli, Lucknow, Uttar Pradesh 226002, India
| | - Nidhi Srivastava
- National Institute of Pharmaceutical Education and Research, Raebareli, Lucknow, Uttar Pradesh 226002, India
| | - Niranjan Meher
- National Institute of Pharmaceutical Education and Research, Raebareli, Lucknow, Uttar Pradesh 226002, India
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3
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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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Brown A, Brill J, Amini R, Nurmi C, Li Y. Development of Better Aptamers: Structured Library Approaches, Selection Methods, and Chemical Modifications. Angew Chem Int Ed Engl 2024; 63:e202318665. [PMID: 38253971 DOI: 10.1002/anie.202318665] [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: 12/05/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 01/24/2024]
Abstract
Systematic evolution of ligands by exponential enrichment (SELEX) has been used to discover thousands of aptamers since its development in 1990. Aptamers are short single-stranded oligonucleotides capable of binding to targets with high specificity and selectivity through structural recognition. While aptamers offer advantages over other molecular recognition elements such as their ease of production, smaller size, extended shelf-life, and lower immunogenicity, they have yet to show significant success in real-world applications. By analyzing the importance of structured library designs, reviewing different SELEX methodologies, and the effects of chemical modifications, we provide a comprehensive overview on the production of aptamers for applications in drug delivery systems, therapeutics, diagnostics, and molecular imaging.
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Affiliation(s)
- Alex Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Jake Brill
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Ryan Amini
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Connor Nurmi
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
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Sun L, Liu H, Ye Y, Lei Y, Islam R, Tan S, Tong R, Miao YB, Cai L. Smart nanoparticles for cancer therapy. Signal Transduct Target Ther 2023; 8:418. [PMID: 37919282 PMCID: PMC10622502 DOI: 10.1038/s41392-023-01642-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/24/2023] [Accepted: 09/05/2023] [Indexed: 11/04/2023] Open
Abstract
Smart nanoparticles, which can respond to biological cues or be guided by them, are emerging as a promising drug delivery platform for precise cancer treatment. The field of oncology, nanotechnology, and biomedicine has witnessed rapid progress, leading to innovative developments in smart nanoparticles for safer and more effective cancer therapy. In this review, we will highlight recent advancements in smart nanoparticles, including polymeric nanoparticles, dendrimers, micelles, liposomes, protein nanoparticles, cell membrane nanoparticles, mesoporous silica nanoparticles, gold nanoparticles, iron oxide nanoparticles, quantum dots, carbon nanotubes, black phosphorus, MOF nanoparticles, and others. We will focus on their classification, structures, synthesis, and intelligent features. These smart nanoparticles possess the ability to respond to various external and internal stimuli, such as enzymes, pH, temperature, optics, and magnetism, making them intelligent systems. Additionally, this review will explore the latest studies on tumor targeting by functionalizing the surfaces of smart nanoparticles with tumor-specific ligands like antibodies, peptides, transferrin, and folic acid. We will also summarize different types of drug delivery options, including small molecules, peptides, proteins, nucleic acids, and even living cells, for their potential use in cancer therapy. While the potential of smart nanoparticles is promising, we will also acknowledge the challenges and clinical prospects associated with their use. Finally, we will propose a blueprint that involves the use of artificial intelligence-powered nanoparticles in cancer treatment applications. By harnessing the potential of smart nanoparticles, this review aims to usher in a new era of precise and personalized cancer therapy, providing patients with individualized treatment options.
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Affiliation(s)
- Leming Sun
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China
- School of Life Sciences, Engineering Research Center of Chinese Ministry of Education for Biological Diagnosis, Treatment and Protection Technology and Equipment in Special Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Hongmei Liu
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Yanqi Ye
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA, 92121, USA
| | - Yang Lei
- School of Life Sciences, Engineering Research Center of Chinese Ministry of Education for Biological Diagnosis, Treatment and Protection Technology and Equipment in Special Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Rehmat Islam
- School of Life Sciences, Engineering Research Center of Chinese Ministry of Education for Biological Diagnosis, Treatment and Protection Technology and Equipment in Special Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Sumin Tan
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Rongsheng Tong
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Yang-Bao Miao
- Department of Haematology, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China.
| | - Lulu Cai
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China.
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Park H, Lee H, Lee M, Baek C, Park JA, Jang M, Kwon Y, Min J, Lee T. Synthesis of Isolated DNA Aptamer and Its Application of AC-Electrothermal Flow-Based Rapid Biosensor for the Detection of Dengue Virus in a Spiked Sample. Bioconjug Chem 2023; 34:1486-1497. [PMID: 37527337 DOI: 10.1021/acs.bioconjchem.3c00249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Dengue fever is an infectious disease caused by the dengue virus (DENV) and is transmitted by mosquitoes in tropical and subtropical regions. The early detection method at a low cost is essential. To address this, we synthesized the isolated DENV aptamer for fabricating a rapid electrochemical biosensor on a Au interdigitated microgap electrode (AuIMGE). The DENV aptamers were generated using the SELEX (systemic evolution of ligands by exponential enrichment) method for binding to DENV surface envelope proteins. To reduce the manufacturing cost, unnecessary nucleotide sequences were excluded from the isolation process of the DENV aptamer. To reduce the detection time, the alternating current electrothermal flow (ACEF) technique was applied to the fabricated biosensor, which can shorten the detection time to 10 min. The performance of the biosensor was evaluated using cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). In the diluted DENV protein solution, the linear range of the concentrations was from 1 pM to 1 μM and the LOD was 76.7 fM. Moreover, the proposed biosensor detected DENV in a diluted spiked sample at a linear range of 10-6 to 106 TCID50/mL, while the detection performance was proven with an LOD of 1.74 × 10-7 TCID50/mL along with high selectivity.
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Affiliation(s)
- Hanbin Park
- Department of Chemical Engineering, Kwangwoon University, 20 Kwangwoon-Ro, Nowon-Gu, Seoul 01897, Republic of Korea
| | - Hoseok Lee
- Department of Electrical and Computer Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08727, Republic of Korea
| | - Myoungro Lee
- Department of Chemical Engineering, Kwangwoon University, 20 Kwangwoon-Ro, Nowon-Gu, Seoul 01897, Republic of Korea
| | - Changyoon Baek
- School of Integrative Engineering, Chung-Ang University, Heukseok-dong, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Jeong Ah Park
- Department of Chemical Engineering, Kwangwoon University, 20 Kwangwoon-Ro, Nowon-Gu, Seoul 01897, Republic of Korea
| | - Moonbong Jang
- Department of Chemical Engineering, Kwangwoon University, 20 Kwangwoon-Ro, Nowon-Gu, Seoul 01897, Republic of Korea
| | - Yein Kwon
- Department of Chemical Engineering, Kwangwoon University, 20 Kwangwoon-Ro, Nowon-Gu, Seoul 01897, Republic of Korea
| | - Junhong Min
- School of Integrative Engineering, Chung-Ang University, Heukseok-dong, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Taek Lee
- Department of Chemical Engineering, Kwangwoon University, 20 Kwangwoon-Ro, Nowon-Gu, Seoul 01897, Republic of Korea
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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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Thevendran R, Rogini S, Leighton G, Mutombwera A, Shigdar S, Tang TH, Citartan M. The Diagnostic Potential of RNA Aptamers against the NS1 Protein of Dengue Virus Serotype 2. BIOLOGY 2023; 12:biology12050722. [PMID: 37237536 DOI: 10.3390/biology12050722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/24/2023] [Accepted: 03/30/2023] [Indexed: 05/28/2023]
Abstract
Dengue infection, caused by the dengue virus, is a global threat which requires immediate attention and appropriate disease management. The current diagnosis of dengue infection is largely based on viral isolation, RT-PCR and serology-based detection, which are time-consuming and expensive, and require trained personnel. For early diagnosis of dengue, the direct detection of a dengue antigenic target is efficacious, and one such target is NS1. NS1-based detection is primarily antibody-centric and is beset by drawbacks pertaining to antibodies such as the high cost of synthesis and large batch-to-batch variation. Aptamers are potential surrogates of antibodies and are much cheaper, without exhibiting batch-to-batch variation. Given these advantages, we sought to isolate RNA aptamers against the NS1 protein of dengue virus serotype 2. A total of 11 cycles of SELEX were carried out, resulting in two potent aptamers, DENV-3 and DENV-6, with dissociation constant values estimated at 37.57 ± 10.34 nM and 41.40 ± 9.29 nM, respectively. These aptamers can be further miniaturized to TDENV-3 and TDENV-6a with an increased LOD upon their usage in direct ELASA. Moreover, these truncated aptamers are highly specific against the dengue NS1 while showing no cross-reactivity against the NS1 of the Zika virus, the E2 protein of the Chikungunya virus or the LipL32 protein of Leptospira, with target selectivity retained even in human serum. The usage of TDENV-3 as the capturing probe and TDENV-6a as the detection probe underpinned the development of an aptamer-based sandwich ELASA for the detection of dengue NS1. The sensitivity of the sandwich ELASA was further improved with the stabilization of the truncated aptamers and the repeated incubation strategy, which enabled a LOD of 2 nM when used with the target NS1 spiked in human serum diluted at 1:2000.
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Affiliation(s)
- Ramesh Thevendran
- Department of Biomedical Science, Advanced Medical & Dental Institute (AMDI), University Sains Malaysia, Bertam, Kepala Batas 13200, Malaysia
| | - Sivalingam Rogini
- Department of Biomedical Science, Advanced Medical & Dental Institute (AMDI), University Sains Malaysia, Bertam, Kepala Batas 13200, Malaysia
| | - Glenn Leighton
- Hutano Diagnostics Ltd. BioEscalator, Innovation Building, Old Road Campus, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Atherton Mutombwera
- Hutano Diagnostics Ltd. BioEscalator, Innovation Building, Old Road Campus, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Sarah Shigdar
- School of Medicine, Deakin University, Geelong, VIC 3217, Australia
- Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, VIC 3220, Australia
| | - Thean-Hock Tang
- Department of Biomedical Science, Advanced Medical & Dental Institute (AMDI), University Sains Malaysia, Bertam, Kepala Batas 13200, Malaysia
| | - Marimuthu Citartan
- Department of Biomedical Science, Advanced Medical & Dental Institute (AMDI), University Sains Malaysia, Bertam, Kepala Batas 13200, Malaysia
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Pundir M, De Rosa MC, Lobanova L, Abdulmawjood S, Chen X, Papagerakis S, Papagerakis P. Structural properties and binding mechanism of DNA aptamers sensing saliva melatonin for diagnosis and monitoring of circadian clock and sleep disorders. Anal Chim Acta 2023; 1251:340971. [PMID: 36925277 DOI: 10.1016/j.aca.2023.340971] [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: 11/14/2022] [Revised: 01/25/2023] [Accepted: 02/12/2023] [Indexed: 02/17/2023]
Abstract
Circadian desynchrony with the external light-dark cycle influences the rhythmic secretion of melatonin which is among the first signs of circadian rhythm sleep disorders. An accurate dim light melatonin onset (established indicator of circadian rhythm sleep disorders) measurement requires lengthy assays, and antibody affinities alterations, especially in patients with circadian rhythm disorders whose melatonin salivary levels vary significantly, making antibodies detection mostly inadequate. In contrast, aptamers with their numerous advantages (e.g., target selectivity, structural flexibility in tuning binding affinities, small size, etc.) can become preferable biorecognition molecules for salivary melatonin detection with high sensitivity and specificity. This study thoroughly characterizes the structural property and binding mechanism of a single-stranded DNA aptamer full sequence (MLT-C-1) and its truncated versions (MLT-A-2, MLT-A-4) to decipher its optimal characteristics for saliva melatonin detection. We use circular dichroism spectroscopy to determine aptamers' conformational changes under different ionic strengths and showed that aptamers display a hairpin loop structure where few base pairs in the stem play a significant role in melatonin binding and formation of aptamer stabilized structure. Through microscale thermophoresis, aptamers demonstrated a high binding affinity in saliva samples (MLT-C-1F Kd = 12.5 ± 1.7 nM; MLT-A-4F Kd = 11.2 ± 1.6 nM; MLT-A-2F Kd = 2.4 ± 2.8 nM; limit-of-detection achieved in pM, highest sensitivity attained for MLT-A-2F aptamer with the lowest detection limit of 1.35 pM). Our data suggest that aptamers are promising as biorecognition molecules and provide the baseline parameters for the development of an aptamer-based point-of-care diagnostic system for melatonin detection and accurate profiling of its fluctuations in saliva.
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Affiliation(s)
- Meenakshi Pundir
- Laboratory of Precision Oral Health and Chronobiology, College of Dentistry, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada; Division of Biomedical Engineering, University of Saskatchewan, 57 Campus Dr, Saskatoon, S7K 5A9, Canada; Laboratory of Oral, Head and Neck Cancer - Personalized Diagnostics and Therapeutics, Department of Surgery, College of Medicine, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada
| | - Maria C De Rosa
- Department of Chemistry, Faculty of Science, Carleton University, 1125 Colonel by Drive, Ottawa, Ontario, K1S 5B6, Canada.
| | - Liubov Lobanova
- Laboratory of Precision Oral Health and Chronobiology, College of Dentistry, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada
| | - Shahad Abdulmawjood
- Department of Chemistry, Faculty of Science, Carleton University, 1125 Colonel by Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - Xiongbiao Chen
- Division of Biomedical Engineering, University of Saskatchewan, 57 Campus Dr, Saskatoon, S7K 5A9, Canada; Department of Mechanical Engineering, School of Engineering, University of Saskatchewan, 57 Campus Dr, S7K 5A9, Saskatoon, Canada.
| | - Silvana Papagerakis
- Laboratory of Precision Oral Health and Chronobiology, College of Dentistry, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada; Laboratory of Oral, Head and Neck Cancer - Personalized Diagnostics and Therapeutics, Department of Surgery, College of Medicine, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada; Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Michigan, 1500 E Medical Center Dr, Ann Arbor, MI, 48109, United States.
| | - Petros Papagerakis
- Laboratory of Precision Oral Health and Chronobiology, College of Dentistry, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada; Division of Biomedical Engineering, University of Saskatchewan, 57 Campus Dr, Saskatoon, S7K 5A9, Canada.
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Uddin N, Binzel DW, Shu D, Fu TM, Guo P. Targeted delivery of RNAi to cancer cells using RNA-ligand displaying exosome. Acta Pharm Sin B 2023; 13:1383-1399. [PMID: 37139430 PMCID: PMC10149909 DOI: 10.1016/j.apsb.2022.11.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/27/2022] [Accepted: 10/13/2022] [Indexed: 11/18/2022] Open
Abstract
Exosome is an excellent vesicle for in vivo delivery of therapeutics, including RNAi and chemical drugs. The extremely high efficiency in cancer regression can partly be attributed to its fusion mechanism in delivering therapeutics to cytosol without endosome trapping. However, being composed of a lipid-bilayer membrane without specific recognition capacity for aimed-cells, the entry into nonspecific cells can lead to potential side-effects and toxicity. Applying engineering approaches for targeting-capacity to deliver therapeutics to specific cells is desirable. Techniques with chemical modification in vitro and genetic engineering in cells have been reported to decorate exosomes with targeting ligands. RNA nanoparticles have been used to harbor tumor-specific ligands displayed on exosome surface. The negative charge reduces nonspecific binding to vital cells with negatively charged lipid-membrane due to the electrostatic repulsion, thus lowering the side-effect and toxicity. In this review, we focus on the uniqueness of RNA nanoparticles for exosome surface display of chemical ligands, small peptides or RNA aptamers, for specific cancer targeting to deliver anticancer therapeutics, highlighting recent advances in targeted delivery of siRNA and miRNA that overcomes the previous RNAi delivery roadblocks. Proper understanding of exosome engineering with RNA nanotechnology promises efficient therapies for a wide range of cancer subtypes.
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Affiliation(s)
- Nasir Uddin
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmacology, College of Pharmacy, the Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA
- James Comprehensive Cancer Center, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Daniel W. Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmacology, College of Pharmacy, the Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA
- James Comprehensive Cancer Center, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Dan Shu
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmacology, College of Pharmacy, the Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA
- James Comprehensive Cancer Center, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Tian-Min Fu
- Department of Biological Chemistry & Pharmacology, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmacology, College of Pharmacy, the Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA
- James Comprehensive Cancer Center, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
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11
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Shien Yeoh T, Yusof Hazrina H, Bukari BA, Tang TH, Citartan M. Generation of an RNA aptamer against LipL32 of Leptospira isolated by Tripartite-hybrid SELEX coupled with in-house Python-aided unbiased data sorting. Bioorg Med Chem 2023; 81:117186. [PMID: 36812779 DOI: 10.1016/j.bmc.2023.117186] [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: 04/27/2022] [Revised: 01/16/2023] [Accepted: 01/23/2023] [Indexed: 02/05/2023]
Abstract
Leptospirosis is a potentially life-threatening zoonosis caused by pathogenic Leptospira. The major hurdle of the diagnosis of Leptospirosis lies in the issues associated with current methods of detection, which are time-consuming, tedious and the need for sophisticated, special equipments. Restrategizing the diagnostics of Leptospirosis may involve considerations of the direct detection of the outer membrane protein, which can be faster, cost-saving and require fewer equipments. One such promising marker is LipL32, which is an antigen with high amino acid sequence conservation among all the pathogenic strains. In this study, we endeavored to isolate an aptamer against LipL32 protein via a modified SELEX strategy known as tripartite-hybrid SELEX, based on 3 different partitioning strategies. In this study, we also demonstrated the deconvolution of the candidate aptamers by using in-house Python-aided unbiased data sorting in examining multiple parameters to isolate potent aptamers. We have successfully generated an RNA aptamer against LipL32 of Leptospira, LepRapt-11, which is applicable in a simple direct ELASA for the detection of LipL32. LepRapt-11 can be a promising molecular recognition element for the diagnosis of leptospirosis by targeting LipL32.
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Affiliation(s)
- Tzi Shien Yeoh
- Department of Biomedical Science, Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia
| | - Hamdani Yusof Hazrina
- Department of Biomedical Science, Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia
| | - Bakhtiar A Bukari
- School of Medicine, Deakin University, 3216 Geelong, Victoria, Australia
| | - Thean-Hock Tang
- Department of Biomedical Science, Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia
| | - Marimuthu Citartan
- Department of Biomedical Science, Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia.
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12
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Liu F, Zhang C, Duan Y, Ma J, Wang Y, Chen G. Optimization of an aptamer against Prorocentrum minimum - A common harmful algae by truncation and G-quadruplex-forming mutation. ENVIRONMENTAL RESEARCH 2023; 220:115099. [PMID: 36563978 DOI: 10.1016/j.envres.2022.115099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/22/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Harmful algal blooms (HABs) caused by Prorocentrum minimum have seriously posed economic losses and ecological disasters. To reduce these losses, aptamers are used as a new molecular probe to establish rapid methods. Herein, to improve the affinity and application of aptamers in the detection of harmful algae, the optimization was performed on the previously reported aptamers against P. minimum. First, a total of seven candidate aptamers, including three truncated aptamers (TA1, TA2 and TA3) and four mutant aptamers (MA1, MA2, MA3 and MA4), were obtained by truncation and G-quadruplex (GQ)-forming mutation. Next, the specificity and affinity test by flow cytometry revealed that except for TA1 and TA2, all of the candidate aptamers are specific with the equilibrium dissociation constant of (40.4 ± 5.5) nM for TA3, (63.3 ± 24.0) nM for MA1, (71.7 ± 14.6) nM for MA2, (365.9 ± 74.4) nM for MA3, and (21.1 ± 0.5) nM for MA4, respectively. The circular dichroism analysis of the mutant aptamers demonstrated that the GQ structures formed by MA1/MA2, MA3 and MA4 were antiparallel, mixed parallel and parallel, respectively. The affinity of aptamers with various GQ is in the order of parallel structure > antiparallel structure > mixed parallel structure. In addition, to further improve binding ability, the binding conditions of MA4 were optimized as follows: binding time, 60 min; binding temperature, 37 °C; pH of the binding buffer, 7.5; and Na+/Mg2+ concentration in the binding buffer, 100 mM/0.5 mM. The binding examination by fluorescence microscopy showed that MA4 had a stronger binding ability to P. minimum than the original aptamer. Taken together, this study not only obtained an aptamer with higher affinity than the original aptamer, which laid a good foundation for subsequent application, but also may provide a feasible reference method for aptamer optimization.
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Affiliation(s)
- Fuguo Liu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Chunyun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China
| | - Yu Duan
- School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Jinju Ma
- School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Yuanyuan Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China.
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13
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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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14
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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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15
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da Silva AG, Goulart LR, Löffler P, Code C, Neves AF. Development of a Molecular Aptamer Beacon Applied to Magnetic-Assisted RNA Extraction for Detection of Dengue and Zika Viruses Using Clinical Samples. Int J Mol Sci 2022; 23:ijms232213866. [PMID: 36430340 PMCID: PMC9693377 DOI: 10.3390/ijms232213866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 11/12/2022] Open
Abstract
Limitations in the detection of cocirculating flaviviruses such as Dengue and Zika lead us to propose the use of aptameric capture of the viral RNA in combination with RT-PCR (APTA-RT-PCR). Aptamers were obtained via SELEX and next-generation sequencing, followed by colorimetric and fluorescent characterizations. An APTA-RT-PCR assay was developed, optimized, and tested against the viral RNAs in 108 serum samples. After selection, sequence APTAZC10 was designed as a bifunctional molecular beacon (APTAZC10-MB), exhibiting affinity for the viral targets. APTA-RT-PCR was able to detect Dengue and Zika RNA in 43% and 8% of samples, respectively. Our results indicate that APTAZC10-MB and APTA-RT-PCR will be useful to improve the detection of Dengue and Zika viruses in a fast molecular assay for the improvement of infectious disease surveillance.
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Affiliation(s)
- Amanda Gabrielle da Silva
- Institute of Physics, Postgraduate Program in Exact and Technological Sciences, Universidade Federal de Catalão, Catalão 75704-020, Brazil
| | - Luiz Ricardo Goulart
- Nanobiotechnology Laboratory, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia 38402-022, Brazil
| | - Philipp Löffler
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Christian Code
- Dianox ApS, Fruebjergvej 3, 2100 København, Denmark
- PhyLife Physical Life Sciences, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Adriana Freitas Neves
- Institute of Biotechnology, Molecular Biology Laboratory, Universidade Federal de Catalão, Catalão 75704-020, Brazil
- Correspondence:
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16
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Wu W, Sun Q, Li T, Liu K, Jiang Y, Wang Y, Yang Y. Selection and characterization of bispecific aptamers against malachite green and leucomalachite green. Anal Biochem 2022; 658:114849. [PMID: 36150472 DOI: 10.1016/j.ab.2022.114849] [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: 04/06/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/01/2022]
Abstract
In order to develop multi-residues rapid detection, the bispecific aptamers against malachite green (MG) and leucomalachite green (LMG) were isolated by the capture systematic evolution of ligands by exponential enrichment (Capture-SELEX). After thirteen rounds of selection, the enriched ssDNA pools were sent for high-throughput sequencing. Nine aptamer candidates (A1-A9) were picked out to test their specificity by gold nanoparticles (AuNPs) colorimetric assay. Three aptamers (A2, A3, A5) with good selectivity were truncated to verify their affinity by fluorescence assay. Finally, three truncated aptamers (A2-a, A3-a, A5-a) with bispecificity and high affinity were identified. For LMG, the dissociation constant (Kd) of them were 8.4 ± 0.8 nM, 8.2 ± 1.2 nM, and 13.7 ± 1.4 nM, respectively. For MG, Kd of them were 3.4 ± 0.3 μM, 2.3 ± 0.2 μM, 3.0 ± 0.2μM. Among them, A3-a is the best. Our work will provide novel probes for the development of multi-residues rapid detection as well as opportunities for multiple target aptamer discovery.
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Affiliation(s)
- Wenwei Wu
- Agricultural College, Yanbian University, Yanji, 133002, China
| | - Qifeng Sun
- Beijing Hightrust Medical Laboratory Co., LTD, Beijing, 102600, China
| | - Tiansong Li
- College of Science, Beihua University, Jilin, 132001, China
| | - Kexin Liu
- Agricultural College, Yanbian University, Yanji, 133002, China
| | - Yan Jiang
- Agricultural College, Yanbian University, Yanji, 133002, China
| | - Yi Wang
- College of Science, Beihua University, Jilin, 132001, China.
| | - Yongjie Yang
- Agricultural College, Yanbian University, Yanji, 133002, China.
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17
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He Y, Xu W, Xiao YT, Huang H, Gu D, Ren S. Targeting signaling pathways in prostate cancer: mechanisms and clinical trials. Signal Transduct Target Ther 2022; 7:198. [PMID: 35750683 PMCID: PMC9232569 DOI: 10.1038/s41392-022-01042-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 12/11/2022] Open
Abstract
Prostate cancer (PCa) affects millions of men globally. Due to advances in understanding genomic landscapes and biological functions, the treatment of PCa continues to improve. Recently, various new classes of agents, which include next-generation androgen receptor (AR) signaling inhibitors (abiraterone, enzalutamide, apalutamide, and darolutamide), bone-targeting agents (radium-223 chloride, zoledronic acid), and poly(ADP-ribose) polymerase (PARP) inhibitors (olaparib, rucaparib, and talazoparib) have been developed to treat PCa. Agents targeting other signaling pathways, including cyclin-dependent kinase (CDK)4/6, Ak strain transforming (AKT), wingless-type protein (WNT), and epigenetic marks, have successively entered clinical trials. Furthermore, prostate-specific membrane antigen (PSMA) targeting agents such as 177Lu-PSMA-617 are promising theranostics that could improve both diagnostic accuracy and therapeutic efficacy. Advanced clinical studies with immune checkpoint inhibitors (ICIs) have shown limited benefits in PCa, whereas subgroups of PCa with mismatch repair (MMR) or CDK12 inactivation may benefit from ICIs treatment. In this review, we summarized the targeted agents of PCa in clinical trials and their underlying mechanisms, and further discussed their limitations and future directions.
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Affiliation(s)
- Yundong He
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China.
| | - Weidong Xu
- Department of Urology, Shanghai Changzheng Hospital, Shanghai, China
| | - Yu-Tian Xiao
- Department of Urology, Shanghai Changzheng Hospital, Shanghai, China.,Department of Urology, Shanghai Changhai Hospital, Shanghai, China
| | - Haojie Huang
- Department of Urology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Di Gu
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Shancheng Ren
- Department of Urology, Shanghai Changzheng Hospital, Shanghai, China.
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18
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Camorani S, d’Argenio A, Agnello L, Nilo R, Zannetti A, Ibarra LE, Fedele M, Cerchia L. Optimization of Short RNA Aptamers for TNBC Cell Targeting. Int J Mol Sci 2022; 23:3511. [PMID: 35408872 PMCID: PMC8998535 DOI: 10.3390/ijms23073511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 02/07/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive cancer with limited targeted therapies. RNA aptamers, suitably chemically modified, work for therapeutic purposes in the same way as antibodies. We recently generated 2'Fluoro-pyrimidines RNA-aptamers that act as effective recognition elements for functional surface signatures of TNBC cells. Here, we optimized three of them by shortening and proved the truncated aptamers as optimal candidates to enable active targeting to TNBC. By using prediction of secondary structure to guide truncation, we identified structural regions that account for the binding motifs of the full-length aptamers. Their chemical synthesis led to short aptamers with superb nuclease resistance, which specifically bind to TNBC target cells and rapidly internalize into acidic compartments. They interfere with the growth of TNBC cells as mammospheres, thus confirming their potential as anti-tumor agents. We propose sTN145, sTN58 and sTN29 aptamers as valuable tools for selective TNBC targeting and promising candidates for effective treatments, including therapeutic agents and targeted delivery nanovectors.
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Affiliation(s)
- Simona Camorani
- National Research Council (CNR), Institute of Experimental Endocrinology and Oncology “Gaetano Salvatore” (IEOS), 80131 Naples, Italy; (A.d.); (L.A.); (R.N.); (M.F.)
| | - Annachiara d’Argenio
- National Research Council (CNR), Institute of Experimental Endocrinology and Oncology “Gaetano Salvatore” (IEOS), 80131 Naples, Italy; (A.d.); (L.A.); (R.N.); (M.F.)
| | - Lisa Agnello
- National Research Council (CNR), Institute of Experimental Endocrinology and Oncology “Gaetano Salvatore” (IEOS), 80131 Naples, Italy; (A.d.); (L.A.); (R.N.); (M.F.)
- Department of Precision Medicine, University of Campania “L. Vanvitelli”, 80138 Naples, Italy
| | - Roberto Nilo
- National Research Council (CNR), Institute of Experimental Endocrinology and Oncology “Gaetano Salvatore” (IEOS), 80131 Naples, Italy; (A.d.); (L.A.); (R.N.); (M.F.)
| | - Antonella Zannetti
- National Research Council (CNR), Institute of Biostructures and Bioimaging (IBB), 80145 Naples, Italy;
| | - Luis Exequiel Ibarra
- Institute of Environmental Biotechnology and Health (INBIAS), National University of Rio Cuarto (UNRC), National Council for Scientific and Technological Research (CONICET), Río Cuarto X5800BIA, Argentina;
| | - Monica Fedele
- National Research Council (CNR), Institute of Experimental Endocrinology and Oncology “Gaetano Salvatore” (IEOS), 80131 Naples, Italy; (A.d.); (L.A.); (R.N.); (M.F.)
| | - Laura Cerchia
- National Research Council (CNR), Institute of Experimental Endocrinology and Oncology “Gaetano Salvatore” (IEOS), 80131 Naples, Italy; (A.d.); (L.A.); (R.N.); (M.F.)
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19
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Wang F, Li Z, Feng X, Yang D, Lin M. Advances in PSMA-targeted therapy for prostate cancer. Prostate Cancer Prostatic Dis 2022; 25:11-26. [PMID: 34050265 DOI: 10.1038/s41391-021-00394-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/27/2021] [Accepted: 05/12/2021] [Indexed: 02/04/2023]
Abstract
Prostate-specific membrane antigen (PSMA), a transmembrane glycoprotein located on the cell membrane, is specifically and highly expressed in prostate cancer (PCa). Besides, its expression level is related to tumor invasiveness. As a molecular target of PCa, PSMA has been extensively studied in the past two decades. Currently, a great deal of evidence suggests that significant progresses have been made in the PSMA-targeted therapy of PCa. Herein, different PSMA-targeted therapies for PCa are reviewed, including radioligand therapy (177Lu-PSMA-RLT, 225Ac-PSMA-RLT), antibody-drug conjugates (MLN2704, PSMA-MMAE, MEDI3726), cellular immunotherapy (CAR-T, CAR/NK-92, PSMA-targeted BiTE), photodynamic therapy, imaging-guided surgery (radionuclide-guided surgery, fluorescence-guided surgery, multimodal imaging-guided surgery), and ultrasound-mediated nanobubble destruction.
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Affiliation(s)
- Fujin Wang
- Nantong University, Nantong, Jiangsu, China.,Department of Radiology, the First People's Hospital of Yancheng, Yancheng, Jiangsu, China
| | - Zhifeng Li
- Nantong University, Nantong, Jiangsu, China
| | - Xiaoqian Feng
- Nantong University, Nantong, Jiangsu, China.,Department of Radiology, the First People's Hospital of Yancheng, Yancheng, Jiangsu, China
| | | | - Mei Lin
- Taizhou People's Hospital Affiliated to Nantong University, Taizhou, Jiangsu, China.
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20
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Metamorphosis of prostate specific membrane antigen (PSMA) inhibitors. Biophys Rev 2022; 14:303-315. [PMID: 35340601 PMCID: PMC8921357 DOI: 10.1007/s12551-021-00919-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/18/2021] [Indexed: 01/16/2023] Open
Abstract
Prostate-specific membrane antigen (PSMA), also called glutamate carboxypeptidase II (GCP(II)), is a Zn-dependent metalloprotease that is known as a well prostate cancer indication and a potential targeting towards anti-cancer medicines and drug delivery. Because of its centrality in the diagnostics and treatment of prostate cancer, several types of inhibitors are designed with particular scaffolds. In this study, important groups of related inhibitors as well as reported experimental and computational studies are being reviewed, in which we examined three functional groups on each group of structures. The importance of computational biochemistry and the necessity of extensive research in this area on PSMA and its effective ligands are recommended.
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21
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Vandghanooni S, Sanaat Z, Farahzadi R, Eskandani M, Omidian H, Omidi Y. Recent progress in the development of aptasensors for cancer diagnosis: Focusing on aptamers against cancer biomarkers. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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22
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Kelly L, Maier KE, Yan A, Levy M. A comparative analysis of cell surface targeting aptamers. Nat Commun 2021; 12:6275. [PMID: 34725326 PMCID: PMC8560833 DOI: 10.1038/s41467-021-26463-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 10/05/2021] [Indexed: 11/10/2022] Open
Abstract
Aptamers represent a potentially important class of ligands for the development of diagnostics and therapeutics. However, it is often difficult to compare the function and specificity of many of these molecules as assay formats and conditions vary greatly. Here, with an interest in developing aptamer targeted therapeutics that could effectively deliver cargoes to cells, we chemically synthesize 15 aptamers that have been reported to target cell surface receptors or cells. Using standardized assay conditions, we assess each aptamer’s binding properties on a panel of 11 different cancer cell lines, correlate aptamer binding to antibody controls and use siRNA transfection to validate each aptamer’s binding to reported target receptors. Using a subset of these molecules known to be expressed on prostate cancers, we use near-infrared in vivo imaging to assess the tumor localization following intravenous injection. Our data demonstrate some surprising differences in the reported specificity and function for many of these molecules and raise concerns regarding their cell targeting capabilities. They also identify an anti-human transferrin aptamer, Waz, as a robust candidate for targeting prostate cancers and for future development of aptamer-based therapeutics. Aptamers could potentially be widely used in therapy and diagnostics. Here the authors use standardised assay conditions to compare aptamer properties in tumour targeting.
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Affiliation(s)
- Linsley Kelly
- Department of Biochemistry, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY, 10461, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Keith E Maier
- Department of Biochemistry, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY, 10461, USA.,EpiCypher Inc, Durham, NC, 27709, USA
| | - Amy Yan
- Department of Biochemistry, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY, 10461, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Matthew Levy
- Department of Biochemistry, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY, 10461, USA. .,Creyon Bio, Inc., San Diego, CA, 92121, USA.
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23
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Binzel DW, Li X, Burns N, Khan E, Lee WJ, Chen LC, Ellipilli S, Miles W, Ho YS, Guo P. Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity. Chem Rev 2021; 121:7398-7467. [PMID: 34038115 PMCID: PMC8312718 DOI: 10.1021/acs.chemrev.1c00009] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA nanotechnology is the bottom-up self-assembly of nanometer-scale architectures, resembling LEGOs, composed mainly of RNA. The ideal building material should be (1) versatile and controllable in shape and stoichiometry, (2) spontaneously self-assemble, and (3) thermodynamically, chemically, and enzymatically stable with a long shelf life. RNA building blocks exhibit each of the above. RNA is a polynucleic acid, making it a polymer, and its negative-charge prevents nonspecific binding to negatively charged cell membranes. The thermostability makes it suitable for logic gates, resistive memory, sensor set-ups, and NEM devices. RNA can be designed and manipulated with a level of simplicity of DNA while displaying versatile structure and enzyme activity of proteins. RNA can fold into single-stranded loops or bulges to serve as mounting dovetails for intermolecular or domain interactions without external linking dowels. RNA nanoparticles display rubber- and amoeba-like properties and are stretchable and shrinkable through multiple repeats, leading to enhanced tumor targeting and fast renal excretion to reduce toxicities. It was predicted in 2014 that RNA would be the third milestone in pharmaceutical drug development. The recent approval of several RNA drugs and COVID-19 mRNA vaccines by FDA suggests that this milestone is being realized. Here, we review the unique properties of RNA nanotechnology, summarize its recent advancements, describe its distinct attributes inside or outside the body and discuss potential applications in nanotechnology, medicine, and material science.
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Affiliation(s)
- Daniel W Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xin Li
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Eshan Khan
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wen-Jui Lee
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Li-Ching Chen
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Satheesh Ellipilli
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wayne Miles
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuan Soon Ho
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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De novo ssRNA Aptamers against the SARS-CoV-2 Main Protease: In Silico Design and Molecular Dynamics Simulation. Int J Mol Sci 2021; 22:ijms22136874. [PMID: 34206794 PMCID: PMC8267631 DOI: 10.3390/ijms22136874] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 12/13/2022] Open
Abstract
Herein, we have generated ssRNA aptamers to inhibit SARS-CoV-2 Mpro, a protease necessary for the SARS-CoV-2 coronavirus replication. Because there is no aptamer 3D structure currently available in the databanks for this protein, first, we modeled an ssRNA aptamer using an entropic fragment-based strategy. We refined the initial sequence and 3D structure by using two sequential approaches, consisting of an elitist genetic algorithm and an RNA inverse process. We identified three specific aptamers against SARS-CoV-2 Mpro, called MAptapro, MAptapro-IR1, and MAptapro-IR2, with similar 3D conformations and that fall in the dimerization region of the SARS-CoV-2 Mpro necessary for the enzymatic activity. Through the molecular dynamic simulation and binding free energy calculation, the interaction between the MAptapro-IR1 aptamer and the SARS-CoV-2 Mpro enzyme resulted in the strongest and the highest stable complex; therefore, the ssRNA MAptapro-IR1 aptamer was selected as the best potential candidate for the inhibition of SARS-CoV-2 Mpro and a perspective therapeutic drug for the COVID-19 disease.
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25
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Determination of minimal sequence for zearalenone aptamer by computational docking and application on an indirect competitive electrochemical aptasensor. Anal Bioanal Chem 2021; 413:3861-3872. [PMID: 34021369 DOI: 10.1007/s00216-021-03336-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/28/2021] [Accepted: 04/09/2021] [Indexed: 10/21/2022]
Abstract
Aptamers are short single-stranded oligonucleotides (either DNA or RNA) that can fold into well-defined three-dimensional (3D) spatial structures which enable them to capture their specific target by complementary shape interactions. Aptamers are selected from large random libraries through the SELEX process and only a small fraction of the sequence is involved in direct docking with the target. In this paper, we describe the possible truncation variants of zearalenone (ZEA) aptamer which might be an effective binding region for the target. The originally selected zearalenone (ZEA) aptamer was 80-mer in length and shown to bind the target with a high affinity (Kd = 41 ± 5 nM). Herein, computational docking simulation was performed with 15 truncated variants to determine the predicted binding energy and responsible binding site of the aptamer-analyte complex. The results revealed that 5 truncated variants had binding energy lower than - 7.0 kcal/mol. Circular dichroism analysis was performed on the shortlisted aptamer and the conformational change of aptamers was observed with the presence of an analyte. Aptamer Z3IN (29-mer) was chosen as the most enhanced affinity for its target with a dissociation constant of 11.77 ± 1.44 nM. The aptamer was further applied in the electrochemical aptasensor of ZEA based on an indirect competitive format. The results demonstrated that the truncated aptamer leads to an enhancement of the sensitivity of the biosensor.
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26
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Chen Z, Hu L, Zhang BT, Lu A, Wang Y, Yu Y, Zhang G. Artificial Intelligence in Aptamer-Target Binding Prediction. Int J Mol Sci 2021; 22:3605. [PMID: 33808496 PMCID: PMC8038094 DOI: 10.3390/ijms22073605] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/18/2022] Open
Abstract
Aptamers are short single-stranded DNA, RNA, or synthetic Xeno nucleic acids (XNA) molecules that can interact with corresponding targets with high affinity. Owing to their unique features, including low cost of production, easy chemical modification, high thermal stability, reproducibility, as well as low levels of immunogenicity and toxicity, aptamers can be used as an alternative to antibodies in diagnostics and therapeutics. Systematic evolution of ligands by exponential enrichment (SELEX), an experimental approach for aptamer screening, allows the selection and identification of in vitro aptamers with high affinity and specificity. However, the SELEX process is time consuming and characterization of the representative aptamer candidates from SELEX is rather laborious. Artificial intelligence (AI) could help to rapidly identify the potential aptamer candidates from a vast number of sequences. This review discusses the advancements of AI pipelines/methods, including structure-based and machine/deep learning-based methods, for predicting the binding ability of aptamers to targets. Structure-based methods are the most used in computer-aided drug design. For this part, we review the secondary and tertiary structure prediction methods for aptamers, molecular docking, as well as molecular dynamic simulation methods for aptamer-target binding. We also performed analysis to compare the accuracy of different secondary and tertiary structure prediction methods for aptamers. On the other hand, advanced machine-/deep-learning models have witnessed successes in predicting the binding abilities between targets and ligands in drug discovery and thus potentially offer a robust and accurate approach to predict the binding between aptamers and targets. The research utilizing machine-/deep-learning techniques for prediction of aptamer-target binding is limited currently. Therefore, perspectives for models, algorithms, and implementation strategies of machine/deep learning-based methods are discussed. This review could facilitate the development and application of high-throughput and less laborious in silico methods in aptamer selection and characterization.
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Affiliation(s)
- Zihao Chen
- School of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong, China; (Z.C.); (B.-T.Z.)
| | - Long Hu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China;
| | - Bao-Ting Zhang
- School of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong, China; (Z.C.); (B.-T.Z.)
| | - Aiping Lu
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China;
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, China
| | - Yaofeng Wang
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong, China
| | - Yuanyuan Yu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, 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
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, 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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27
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Weaver SD, Whelan RJ. Characterization of DNA aptamer-protein binding using fluorescence anisotropy assays in low-volume, high-efficiency plates. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:1302-1307. [PMID: 33533761 DOI: 10.1039/d0ay02256j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Aptamers have many useful attributes including specific binding to molecular targets. After aptamers are identified, their target binding must be characterized. Fluorescence anisotropy (FA) is one technique that can be used to characterize affinity and to optimize aptamer-target interactions. Efforts to make FA assays more efficient by reducing assay volume and time from mixing to measurement may save time and resources by minimizing consumption of costly reagents. Here, we use thrombin and two thrombin-binding aptamers as a model system to show that plate-based FA experiments can be performed in volumes as low as 2 μL per well with 20 minute incubations with minimal loss in assay precision. We demonstrate that the aptamer-thrombin interaction is best modelled with the Hill equation, indicating cooperative binding. The miniaturization of this assay has implications in drug development, as well as in the efficiency of aptamer selection workflows by allowing for higher throughput aptamer analysis.
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Affiliation(s)
- Simon D Weaver
- Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, IN, USA
| | - Rebecca J Whelan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA.
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28
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Improved Cancer Targeting by Multimerizing Aptamers on Nanoscaffolds. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 22:994-1003. [PMID: 33251048 PMCID: PMC7679244 DOI: 10.1016/j.omtn.2020.10.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/10/2020] [Indexed: 11/24/2022]
Abstract
Aptamers are short single-stranded oligonucleotides selected to bind with high affinity and specificity to a target. In contrast to antibodies, aptamers can be produced in large-scale in vitro systems without the need for any biological agents, making them highly attractive as targeting ligands for bioimaging and drug delivery. For in vivo applications it is often desirable to multimerize the aptamers in order to increase their binding strength and overall specificity. Additional functionalities, such as imaging and therapeutic agents, as well as pharmacokinetic modifiers, need to be attached in a stoichiometric fashion. Herein, we present a robust method for assembly of up to three aptamers and a fluorophore in a single well-defined nanostructure. The process is entirely modular and can be applied to any aptamer requiring only a single reactive "click handle." Multimerization of two aptamers, A9g and GL21.T, previously shown to target cancer cells, led to a strong increase in cell uptake. A similar effect was observed for the prostate-specific membrane antigen (PSMA)-targeting A9g aptamer in mice where multivalent aptamer binding led to increased tumor specificity. Altogether, this method provides a platform for multimerization of aptamers with advantages in terms of combinatorial screening capacity and multifunctional design of nanomedicine.
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29
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Ptacek J, Zhang D, Qiu L, Kruspe S, Motlova L, Kolenko P, Novakova Z, Shubham S, Havlinova B, Baranova P, Chen SJ, Zou X, Giangrande P, Barinka C. Structural basis of prostate-specific membrane antigen recognition by the A9g RNA aptamer. Nucleic Acids Res 2020; 48:11130-11145. [PMID: 32525981 PMCID: PMC7641732 DOI: 10.1093/nar/gkaa494] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 05/27/2020] [Accepted: 06/01/2020] [Indexed: 12/24/2022] Open
Abstract
Prostate-specific membrane antigen (PSMA) is a well-characterized tumor marker associated with prostate cancer and neovasculature of most solid tumors. PSMA-specific ligands are thus being developed to deliver imaging or therapeutic agents to cancer cells. Here, we report on a crystal structure of human PSMA in complex with A9g, a 43-bp PSMA-specific RNA aptamer, that was determined to the 2.2 Å resolution limit. The analysis of the PSMA/aptamer interface allows for identification of key interactions critical for nanomolar binding affinity and high selectivity of A9g for human PSMA. Combined with in silico modeling, site-directed mutagenesis, inhibition experiments and cell-based assays, the structure also provides an insight into structural changes of the aptamer and PSMA upon complex formation, mechanistic explanation for inhibition of the PSMA enzymatic activity by A9g as well as its ligand-selective competition with small molecules targeting the internal pocket of the enzyme. Additionally, comparison with published protein-RNA aptamer structures pointed toward more general features governing protein-aptamer interactions. Finally, our findings can be exploited for the structure-assisted design of future A9g-based derivatives with improved binding and stability characteristics.
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Affiliation(s)
- Jakub Ptacek
- Laboratory of Structural Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, Vestec 25250, Czech Republic
| | - Dong Zhang
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, USA
| | - Liming Qiu
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, USA
| | - Sven Kruspe
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Lucia Motlova
- Laboratory of Structural Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, Vestec 25250, Czech Republic
| | - Petr Kolenko
- Laboratory of Structural Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, Vestec 25250, Czech Republic.,Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Brehova 7, Prague 11519, Czech Republic
| | - Zora Novakova
- Laboratory of Structural Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, Vestec 25250, Czech Republic
| | - Shambhavi Shubham
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Barbora Havlinova
- Laboratory of Structural Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, Vestec 25250, Czech Republic
| | - Petra Baranova
- Laboratory of Structural Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, Vestec 25250, Czech Republic
| | - Shi-Jie Chen
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, USA.,Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Xiaoqin Zou
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, USA.,Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, USA.,Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Paloma Giangrande
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Cyril Barinka
- Laboratory of Structural Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, Vestec 25250, Czech Republic
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30
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Buglak AA, Samokhvalov AV, Zherdev AV, Dzantiev BB. Methods and Applications of In Silico Aptamer Design and Modeling. Int J Mol Sci 2020; 21:E8420. [PMID: 33182550 PMCID: PMC7698023 DOI: 10.3390/ijms21228420] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/04/2020] [Accepted: 11/08/2020] [Indexed: 02/07/2023] Open
Abstract
Aptamers are nucleic acid analogues of antibodies with high affinity to different targets, such as cells, viruses, proteins, inorganic materials, and coenzymes. Empirical approaches allow the design of in vitro aptamers that bind particularly to a target molecule with high affinity and selectivity. Theoretical methods allow significant expansion of the possibilities of aptamer design. In this study, we review theoretical and joint theoretical-experimental studies dedicated to aptamer design and modeling. We consider aptamers with different targets, such as proteins, antibiotics, organophosphates, nucleobases, amino acids, and drugs. During nucleic acid modeling and in silico design, a full set of in silico methods can be applied, such as docking, molecular dynamics (MD), and statistical analysis. The typical modeling workflow starts with structure prediction. Then, docking of target and aptamer is performed. Next, MD simulations are performed, which allows for an evaluation of the stability of aptamer/ligand complexes and determination of the binding energies with higher accuracy. Then, aptamer/ligand interactions are analyzed, and mutations of studied aptamers made. Subsequently, the whole procedure of molecular modeling can be reiterated. Thus, the interactions between aptamers and their ligands are complex and difficult to understand using only experimental approaches. Docking and MD are irreplaceable when aptamers are studied in silico.
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Affiliation(s)
- Andrey A. Buglak
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky prospect 33, 119071 Moscow, Russia; (A.V.S.); (A.V.Z.); (B.B.D.)
- Physical Faculty, St. Petersburg State University, 7/9 Universitetskaya naberezhnaya, 199034 St. Petersburg, Russia
| | - Alexey V. Samokhvalov
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky prospect 33, 119071 Moscow, Russia; (A.V.S.); (A.V.Z.); (B.B.D.)
| | - Anatoly V. Zherdev
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky prospect 33, 119071 Moscow, Russia; (A.V.S.); (A.V.Z.); (B.B.D.)
| | - Boris B. Dzantiev
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky prospect 33, 119071 Moscow, Russia; (A.V.S.); (A.V.Z.); (B.B.D.)
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31
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Jose J, Thomas AM, Mendonsa D, Al-Sanea MM, Uddin MS, Parambi DGT, Charyulu RN, Mathew B. Aptamers in Drug Design: An Emerging Weapon to Fight a Losing Battle. Curr Drug Targets 2020; 20:1624-1635. [PMID: 31362673 DOI: 10.2174/1389450120666190729121747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 11/22/2022]
Abstract
Implementation of novel and biocompatible polymers in drug design is an emerging and rapidly growing area of research. Even though we have a large number of polymer materials for various applications, the biocompatibility of these materials remains as a herculean task for researchers. Aptamers provide a vital and efficient solution to this problem. They are usually small (ranging from 20 to 60 nucleotides, single-stranded DNA or RNA oligonucleotides which are capable of binding to molecules possessing high affinity and other properties like specificity. This review focuses on different aspects of Aptamers in drug discovery, starting from its preparation methods and covering the recent scenario reported in the literature regarding their use in drug discovery. We address the limitations of Aptamers and provide valuable insights into their future potential in the areas regarding drug discovery research. Finally, we explained the major role of Aptamers like medical imaging techniques, application as synthetic antibodies, and the most recent application, which is in combination with nanomedicines.
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Affiliation(s)
- Jobin Jose
- Department of Pharmaceutics, N.G.S.M. Institute of Pharmaceutical Sciences, NITTE Deemed to be University, Mangalore, India
| | - Aaron Mathew Thomas
- Department of Pharmaceutics, N.G.S.M. Institute of Pharmaceutical Sciences, NITTE Deemed to be University, Mangalore, India
| | - Darewin Mendonsa
- Department of Pharmaceutics, N.G.S.M. Institute of Pharmaceutical Sciences, NITTE Deemed to be University, Mangalore, India
| | - Mohammad M Al-Sanea
- College of Pharmacy, Department of Pharmaceutical Chemistry, Jouf University, Sakaka, Al Jouf-2014, Saudi Arabia
| | - Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh.,Pharmakon Neuroscience Research Network, Dhaka, Bangladesh
| | - Della Grace Thomas Parambi
- College of Pharmacy, Department of Pharmaceutical Chemistry, Jouf University, Sakaka, Al Jouf-2014, Saudi Arabia
| | - R Narayana Charyulu
- Department of Pharmaceutics, N.G.S.M. Institute of Pharmaceutical Sciences, NITTE Deemed to be University, Mangalore, India
| | - Bijo Mathew
- Division of Drug Design and Medicinal Chemistry Research Lab, Department of Pharmaceutical Chemistry, Ahalia School of Pharmacy, Palakkad 678557, Kerala, India
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32
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Hashemi M, Shamshiri A, Saeedi M, Tayebi L, Yazdian-Robati R. Aptamer-conjugated PLGA nanoparticles for delivery and imaging of cancer therapeutic drugs. Arch Biochem Biophys 2020; 691:108485. [PMID: 32712288 DOI: 10.1016/j.abb.2020.108485] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 02/07/2023]
Abstract
Most problems associated with chemotherapeutic agents involve non-specific cytotoxicity, low intratumoral accumulation and drug resistance. Targeted drug delivery systems (TDDS) based on nanoparticles (NPs) are a new strategy for better therapeutic efficiency, along with reduction of side effects commonly seen with cancer drugs. Poly (lactic-co-glycolic acid) (PLGA), as one of the furthest developed synthetic polymer, has gained significant attention because of excellent properties-including biodegradability and biocompatibility, controlled release of drug, protection of drug or gene from decomposition and ability to modify surface with targeting agents for both cancer diagnosis and therapy. Aptamers are single-stranded RNA or DNA that can fold through intramolecular interactions into specific three-dimensional structures to selectively and exclusively bind with interested biomarkers. In this review, we explain the latest developments regarding the application of aptamer-decorated PLGA NPs in delivery of therapeutic agents or cancer-related genes into cancer cells. Additionally, we discuss the most recent efforts in the field of aptamer-grafted PLGA-based NPs as theranostics and stimuli-responsive agents.
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Affiliation(s)
- Maryam Hashemi
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad, University of Medical Sciences, Mashhad, Iran
| | | | - Majid Saeedi
- Department of Pharmaceutics, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Lobat Tayebi
- Marquette University School of Dentistry, Milwaukee, WI, 53233, USA.
| | - Rezvan Yazdian-Robati
- Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.
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33
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Yu Y, Dang J, Liu X, Wang L, Li S, Zhang T, Ding X. Metal-Labeled Aptamers as Novel Nanoprobes for Imaging Mass Cytometry Analysis. Anal Chem 2020; 92:6312-6320. [PMID: 32208602 DOI: 10.1021/acs.analchem.9b05159] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Imaging mass cytometry (IMC) is an emerging imaging technology that exploits the multiplexed analysis capabilities of the CyTOF mass cytometer to make spatially resolved measurements for tissue sections. In a comprehensive view of tissue composition and marker distribution, recent developments of IMC require highly sensitive, multiplexed assays. Approaching the sensitivity of the IMC technique, we designed a novel type of biocompatible metal-labeled aptamer nanoprobe (MAP), named 167Er-A10-3.2. The small molecular probe was synthesized by conjugating 167Er-polymeric pentetic acid (167Er-DTPA) with an RNA aptamer A10-3.2. For demonstration, 167Er-A10-3.2 was applied for observing protein spatial distribution on prostatic epithelium cell of paraffin embedded Prostatic adenocarcinoma (PaC) tissue sections by IMC technology. The 167Er-A10-3.2 capitalizes on the ability of the aptamer to specifically bind target cancer cells as well as the small size of 167Er-A10-3.2 can accommodate multiple aptamer binding antigen labeled at high density. The detection signal of 167Er-A10-3.2 probe was 3-fold higher than that of PSMA antibody probe for a targeted cell under lower temperature epitope retrieval (37 °C) of PaC tissue. Furthermore, we successfully demonstrated the simultaneously staining ability of aptamer probes in IMC analysis. The successful imaging acquisition using aptamers probes in IMC technology may offer opportunity for the diagnosis of malignancies in the future.
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Affiliation(s)
- Youyi Yu
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Jingqi Dang
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xiao Liu
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Liping Wang
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Shanhe Li
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Ting Zhang
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xianting Ding
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
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34
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Thevendran R, Sarah S, Tang TH, Citartan M. Strategies to bioengineer aptamer-driven nanovehicles as exceptional molecular tools for targeted therapeutics: A review. J Control Release 2020; 323:530-548. [PMID: 32380206 DOI: 10.1016/j.jconrel.2020.04.051] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 02/06/2023]
Abstract
Aptamers are a class of folded nucleic acid strands capable of binding to different target molecules with high affinity and selectivity. Over the years, they have gained a substantial amount of interest as promising molecular tools for numerous medical applications, particularly in targeted therapeutics. However, only the different treatment approaches and current developments of aptamer-drug therapies have been discussed so far, ignoring the crucial technical and functional aspects of constructing a therapeutically effective aptamer-driven drug delivery system that translates to improved in-vivo performance. Hence, this paper provides a comprehensive review of the strategies used to improve the therapeutic performance of aptamer-guided delivery systems. We focus on the different functional features such as drug deployment, payload capacity, in-vivo stability and targeting efficiency to further our knowledge in enhancing the cell-specific delivery of aptamer-drug conjugates. Each reported strategy is critically discussed to emphasize both the benefits provided in comparison with other similar techniques and to outline their potential drawbacks with respect to the molecular properties of the aptamers, the drug and the system to be designed. The molecular architecture and design considerations for an efficient aptamer-based delivery system are also briefly elaborated.
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Affiliation(s)
- Ramesh Thevendran
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
| | - Shigdar Sarah
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3216, Australia
| | - Thean-Hock Tang
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
| | - Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
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Vandghanooni S, Barar J, Eskandani M, Omidi Y. Aptamer-conjugated mesoporous silica nanoparticles for simultaneous imaging and therapy of cancer. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115759] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Qiu L, Zou X. Scoring Functions for Protein-RNA Complex Structure Prediction: Advances, Applications, and Future Directions. COMMUNICATIONS IN INFORMATION AND SYSTEMS 2020; 20:1-22. [PMID: 33867869 DOI: 10.4310/cis.2020.v20.n1.a1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Protein-RNA interaction is among the most essential of biological events in living cells, being involved in protein synthesizing, RNA processing and transport, DNA transcription, and regulation of gene expression, and many other critical bio-molecular activities. A thorough understanding of this interaction is of paramount importance in fundamental study of a variety of vital cellular processes and therapeutic application for remedy of a broad range of diseases. Experimental high-resolution 3D structure determination is the primary source of knowledge for protein-RNA complexes. However, due to technical limitations, the existing techniques for experimental structure determination couldn't match the demand from fast growing interest in academia and industry. This problem necessitates the alternative high-throughput computational method for protein-RNA complex structure prediction. Similar to the in silico methods used for protein-protein and protein-DNA interactions, a reliable prediction of protein-RNA complex structure requires a scoring function with commensurate discriminatory power. Derived from determined structures and purposed to predict the to-be-determined structures, the scoring function is not only a predictive tool but also a gauge of our knowledge of protein-RNA interaction. In this review, we present an overview of the status of existing scoring functions and the scientific principle behind their constructions as well as their strengths and limitations. Finally, we will discuss about future directions of the scoring function development for protein-RNA structure prediction.
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Affiliation(s)
- Liming Qiu
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211
| | - Xiaoqin Zou
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211.,Department of Physics & Astronomy, University of Missouri, Columbia, Missouri 65211.,Department of Biochemistry, University of Missouri, Columbia, Missouri 65211.,Informatics Institute, University of Missouri, Columbia, Missouri 65211
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Characterization of A Bifunctional Synthetic RNA Aptamer and A Truncated Form for Ability to Inhibit Growth of Non-Small Cell Lung Cancer. Sci Rep 2019; 9:18836. [PMID: 31827170 PMCID: PMC6906461 DOI: 10.1038/s41598-019-55280-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/25/2019] [Indexed: 12/24/2022] Open
Abstract
An in vitro-transcribed RNA aptamer (trans-RA16) that targets non-small cell lung cancer (NSCLC) was previously identified through in vivo SELEX. Trans-RA16 can specifically target and inhibit human NCI-H460 cells in vitro and xenograft tumors in vivo. Here, in a follow-up study, we obtained a chemically-synthesized version of this RNA aptamer (syn-RA16) and a truncated form, and compared them to trans-RA16 for abilities to target and inhibit NCI-H460 cells. The syn-RA16, preferred for drug development, was by design to differ from trans-RA16 in the extents of RNA modifications by biotin, which may affect RA16’s anti-tumor effects. We observed aptamer binding to NCI-H460 cells with KD values of 24.75 ± 2.28 nM and 12.14 ± 1.46 nM for syn-RA16 and trans-RA16, respectively. Similar to trans-RA16, syn-RA16 was capable of inhibiting NCI-H460 cell viability in a dose-dependent manner. IC50 values were 118.4 nM (n = 4) for syn-RA16 and 105.7 nM (n = 4) for trans-RA16. Further studies using syn-RA16 demonstrated its internalization into NCI-H460 cells and inhibition of NCI-H460 cell growth. Moreover, in vivo imaging demonstrated the gradual accumulation of both syn-RA16 and trans-RA16 at the grafted tumor site, and qRT-PCR showed high retention of syn-RA16 in tumor tissues. In addition, a truncated fragment of trans-RA16 (S3) was identified, which exhibited binding affinity for NCI-H460 cells with a KD value of 63.20 ± 0.91 nM and inhibited NCI-H460 cell growth by 39.32 ± 3.25% at 150 nM. These features of the syn-RA16 and S3 aptamers should facilitate the development of a novel diagnostic or treatment approach for NSCLC in clinical settings.
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Heiat M, Negahdary M. Sensitive diagnosis of alpha-fetoprotein by a label free nanoaptasensor designed by modified Au electrode with spindle-shaped gold nanostructure. Microchem J 2019. [DOI: 10.1016/j.microc.2019.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Sullivan R, Adams MC, Naik RR, Milam VT. Analyzing Secondary Structure Patterns in DNA Aptamers Identified via CompELS. Molecules 2019; 24:molecules24081572. [PMID: 31010064 PMCID: PMC6515186 DOI: 10.3390/molecules24081572] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/09/2019] [Accepted: 04/15/2019] [Indexed: 12/12/2022] Open
Abstract
In contrast to sophisticated high-throughput sequencing tools for genomic DNA, analytical tools for comparing secondary structure features between multiple single-stranded DNA sequences are less developed. For single-stranded nucleic acid ligands called aptamers, secondary structure is widely thought to play a pivotal role in driving recognition-based binding activity between an aptamer sequence and its specific target. Here, we employ a competition-based aptamer screening platform called CompELS to identify DNA aptamers for a colloidal target. We then analyze predicted secondary structures of the aptamers and a large population of random sequences to identify sequence features and patterns. Our secondary structure analysis identifies patterns ranging from position-dependent score matrixes of individual structural elements to position-independent consensus domains resulting from global alignment.
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Affiliation(s)
- Richard Sullivan
- School of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Dr. NW, Atlanta, GA 30332-0245, USA.
| | - Mary Catherine Adams
- School of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Dr. NW, Atlanta, GA 30332-0245, USA.
| | - Rajesh R Naik
- 711 Human Performance Wing, Air Force Research Laboratory, Wright Patterson AFB, OH 45433, USA.
| | - Valeria T Milam
- School of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Dr. NW, Atlanta, GA 30332-0245, USA.
- Wallace H. Coulter, Department of Biomedical Engineering, Georgia Institute of Technology, 313 Ferst Dr., Atlanta, GA 30332, USA.
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 315 Ferst Dr., Atlanta, GA 30332-0363, USA.
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Ye H, Duan N, Gu H, Wang H, Wang Z. Fluorometric determination of lipopolysaccharides via changes of the graphene oxide-enhanced fluorescence polarization caused by truncated aptamers. Mikrochim Acta 2019; 186:173. [PMID: 30771102 DOI: 10.1007/s00604-019-3261-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/16/2019] [Indexed: 12/21/2022]
Abstract
A broad-spectrum ssDNA aptamer containing 80 nucleotides (LA80) and capable of binding to four different sources of lipopolysaccharides (LPSs) was truncated. Two strategies are used to produce truncated aptamers of different length. The results show that LA27, a 27-nt aptamer, retained broad-spectrum capability and has a higher affinity (Kd = 46.2 ± 9.5 nM). A graphene oxide based fluorescence polarization assay (excitation/emission wavelengths: 485/520 nm) was worked out using FAM-labeled LA27. It can detect LPSs from Salmonella entericaserotype typhimurium, Pseudomonas aeruginosa 10 and Escherichia coli 055:B5 with enhanced performance (4.8 to 29-fold improvements) compared to LA80. The assay can be performed within 30 min, and the detection limits are 38.7, 88.0 and 154 ng·mL-1, respectively. Graphical abstract Schematic presentation of the assay: A shorter aptamer, with higher affinity than its original aptamer, was obtained by truncated strategies. This core aptamer lead to release easily and enhance the sensivity of the GO-based fluorescence polarization assay.
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Affiliation(s)
- Hua Ye
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- College of Food Engineering, Anhui Science and Technology University, Fengyang, 233100, China
| | - Nuo Duan
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Huajie Gu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Chemical Biology and Materials Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Haitao Wang
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, China.
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China.
- Collaborative Innovation Center of Food safety and Quality Control of Jiangsu Province, Jiangnan University, Wuxi, 214122, China.
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Taheri RA, Eskandari K, Negahdary M. An electrochemical dopamine aptasensor using the modified Au electrode with spindle-shaped gold nanostructure. Microchem J 2018. [DOI: 10.1016/j.microc.2018.08.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Zhou Y, Li W, Tseng Y, Zhang J, Liu J. Developing slow-off dickkopf-1 aptamers for early-diagnosis of hepatocellular carcinoma. Talanta 2018; 194:422-429. [PMID: 30609553 DOI: 10.1016/j.talanta.2018.10.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/25/2018] [Accepted: 10/03/2018] [Indexed: 01/10/2023]
Abstract
In this work, we obtained fast-off and slow-off aptamer recognizing dickkopf-1(DKK1), a promising biomarker for detection of early-stage hepatocellular carcinoma (HCC), with high affinity in a single SELEX procedure. The two types of aptamer possessed distinct characteristics confirmed via different validation methods. In comparison to fast-off aptamers, slow-off aptamers were proven more suitable for aptamer-based ELISA assay. Using slow dissociation SELEX, slow-off aptamers were selectively retained. Meanwhile, a mutant (34del) of slow-off D10 was estimated with picomolar affinity (371.9 pM). The mutant was further truncated into 39nt before pairing with an antibody in the aptamer-based ELISA. The aptamer-target-antibody construction showed similar performance as conventional ELISA with a detection limit of 62.5 pg/ml. Quantification in 60 sera samples with the construction was also correlated with conventional ELISA. The results demonstrated novel DKK1 aptamer could replace capture antibody for potential early HCC diagnosis.
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Affiliation(s)
- Yin Zhou
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Wenshuai Li
- Department of Digestive Diseases of Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200040, China
| | - Yujen Tseng
- Department of Digestive Diseases of Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200040, China
| | - Jun Zhang
- Department of Digestive Diseases of Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200040, China.
| | - Jie Liu
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Digestive Diseases of Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200040, China.
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Tapp MJN, Slocik JM, Dennis PB, Naik RR, Milam VT. Competition-Enhanced Ligand Selection to Identify DNA Aptamers. ACS COMBINATORIAL SCIENCE 2018; 20:585-593. [PMID: 30189130 DOI: 10.1021/acscombsci.8b00048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Competition-enhanced ligand screening (CompELS) was employed to rapidly screen through large DNA libraries to identify single-stranded, oligonucleotide-based ligands called aptamers that bind to a nonbiological target. This previously unreported aptamer screening approach involves the repeated introduction of unenriched random sequence populations during the biopanning process, but avoids iterative elution and polymerase chain reaction (PCR) amplification steps inherent to traditional SELEX (systematic evolution of ligands by exponential enrichment) screening. In this study, 25 aptamers were identified against a gold surface via CompELS and evaluated to identify patterns in primary structures and predicted secondary structures. Following a final one-round competition experiment with the 25 identified aptamers, one particular aptamer sequence (1N) emerged as the most competitive adsorbate species for the gold substrate. Binding analysis indicated at least an order of magnitude difference in the binding affinity of 1N ( Kd = 5.6 × 10-10 M) compared to five other high affinity aptamer candidates ( Kd = 10-8-10-9 M) from identical secondary structure families. Collectively, these studies introduce a rapid, reliable screening and ranking platform along with a classification scheme well-suited for identifying and characterizing aptamers for nonbiological as well as biological targets.
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Affiliation(s)
| | - Joseph M. Slocik
- Materials & Manufacturing Directorate, Soft Matter Materials Branch, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Patrick B. Dennis
- Materials & Manufacturing Directorate, Soft Matter Materials Branch, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Rajesh R. Naik
- Materials & Manufacturing Directorate, Soft Matter Materials Branch, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
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Therapeutic aptamers in discovery, preclinical and clinical stages. Adv Drug Deliv Rev 2018; 134:51-64. [PMID: 30125605 DOI: 10.1016/j.addr.2018.08.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 07/11/2018] [Accepted: 08/16/2018] [Indexed: 02/06/2023]
Abstract
The aptamer field witnessed steady growth during the past 28 years as evident from the exponentially increasing number of related publications. The field is "coming of age", but like other biomedical research areas facing a global push towards translational research to carry ideas from bench- to bedside, there is pressure to show impact for aptamers at the clinical end. Being easy-to-make, non-immunogenic, stable and high-affinity nano-ligands, aptamers are perfectly poised to move in this direction. They can specifically bind targets ranging from small molecules to complex multimeric structures, making them potentially useful in a limitless variety of therapeutic approaches. This review will summarize efforts made to accomplish the therapeutic promise of aptamers, with a focus on aptamers directly acting as therapeutic molecules, rather than those used in targeted delivery of other drugs. The review will showcase representative examples at various stages of development, covering different disease categories.
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Sivakumar P, Kim S, Kang HC, Shim MS. Targeted siRNA delivery using aptamer-siRNA chimeras and aptamer-conjugated nanoparticles. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2018; 11:e1543. [PMID: 30070426 DOI: 10.1002/wnan.1543] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 06/09/2018] [Accepted: 07/10/2018] [Indexed: 12/27/2022]
Abstract
The sequence-specific gene-silencing ability of small interfering RNA (siRNA) has been exploited as a new therapeutic approach for the treatment of a variety of diseases. However, efficient and safe delivery of siRNA into target cells is still a challenge in the clinical development of siRNA-based therapeutics. Recently, nucleic acid-based aptamers that target cell surface proteins have emerged as a new class of targeting moieties due to their high specificity and avidity. To date, various aptamer-mediated siRNA delivery systems have been developed to enhance the RNA interference (RNAi) efficacy of siRNA via targeted delivery. In this review, we summarize recent advances in developing aptamer-mediated siRNA delivery systems for RNAi therapeutics, mainly aptamer-siRNA chimeras and aptamer-functionalized nanocarriers incorporating siRNA, with a focus on their molecular designs and formulations. In addition, the challenges and engineering strategies of aptamer-mediated siRNA delivery systems for clinical translation are discussed. This article is categorized under: Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease.
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Affiliation(s)
- Padmanaban Sivakumar
- Division of Bioengineering, Incheon National University, Incheon, Republic of Korea
| | - Sumin Kim
- Department of Pharmacy, Integrated Research Institute of Pharmaceutical Sciences, and BK21 PLUS Team for Creative Leader Program for Pharmacomics-based Future Pharmacy, College of Pharmacy, The Catholic University of Korea, Gyeonggi-do, Republic of Korea
| | - Han Chang Kang
- Department of Pharmacy, Integrated Research Institute of Pharmaceutical Sciences, and BK21 PLUS Team for Creative Leader Program for Pharmacomics-based Future Pharmacy, College of Pharmacy, The Catholic University of Korea, Gyeonggi-do, Republic of Korea
| | - Min Suk Shim
- Division of Bioengineering, Incheon National University, Incheon, Republic of Korea
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Lupold SE. Aptamers and apple pies: a mini-review of PSMA aptamers and lessons from Donald S. Coffey. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2018; 6:78-86. [PMID: 29666835 PMCID: PMC5902725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 03/19/2018] [Indexed: 06/08/2023]
Abstract
This mini-review article is part of a special issue dedicated to Donald S. Coffey, a pioneer translational research scientist, exemplary mentor, and leader in urologic and urologic oncology research. This article first briefly reflects on life and scientific lessons from Don Coffey. It then reviews the development of two prostate cancer targeting RNA aptamers, xPSM-A9 and xPSM-A10, through in vitro selection for aptamers that bind to the extracellular domain of the Prostate Specific Membrane Antigen (PSMA). These 2'-fluorpyrimidine RNA aptamers selectively bind PSMA on the surface of prostate cancer cells, inhibit PSMA glutamate carboxypeptidase activity, and internalize into PSMA-expressing cancer cells. The truncation of both aptamers, through experimentation as well as logical design, has produced smaller isoforms including A10-3, A10-3.2, A9g and A9L. The larger aptamer isoforms xPSM-A9 and xPSM-A10 are limited to production by in vitro transcription and polyacrylamide gel purification, while smaller isoforms can be generated by chemically synthesis. A series of aptamer conjugates have been developed through chemical crosslinking, complementary annealing strategies, or a combination of both, for the targeting of experimental therapeutics to and into prostate cancer cells. The resulting aptamer conjugates, including nanoparticles and siRNA conjugates, selectively target PSMA-positive prostate cancer cells and xenograft tumors, and demonstrate potent cytotoxic and tumoricidal activity. These experimental therapeutic agents provide a platform for realizing and optimizing the potential of tumor-selective targeting and drug delivery.
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Affiliation(s)
- Shawn E Lupold
- The James Buchanan Brady Urologic Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD, USA; The Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins UniversityBaltimore, MD, USA
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Li K, Deng J, Jin H, Yang X, Fan X, Li L, Zhao Y, Guan Z, Wu Y, Zhang L, Yang Z. Chemical modification improves the stability of the DNA aptamer GBI-10 and its affinity towards tenascin-C. Org Biomol Chem 2018; 15:1174-1182. [PMID: 28084479 DOI: 10.1039/c6ob02577c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aptamers are useful tools in molecular imaging due to their numerous attractive properties, such as excellent affinity and selectivity to diverse types of target molecules and biocompatibility. We carried out structure-activity relationship studies with the tenascin-C (TN-C) binding aptamer GBI-10, which is a promising candidate in tumor imaging. To increase the tumor targeting ability and nuclease resistance under physiological conditions, systematic modifications of GBI-10 with single and multiple 2'-deoxyinosine (2'-dI) or d-/l-isonucleoside (d-/l-isoNA) were performed. Results indicated that sector 3 of the proposed secondary structure is the most important region for specific binding with TN-C. By correlating the affinity of eighty-four GBI-10 derivatives with their predicted secondary structure by Zuker Mfold, we first validated the preferred secondary structure at 37 °C. We found that d-/l-isoNA modified GBI-10 derivatives exhibited improved affinity to the target as well as plasma stability. Affinity measurement and confocal imaging analysis highlighted one potent compound: 4AL/26TL/32TL, which possessed a significantly increased targeting ability to tumor cells. These results revealed the types of modified nucleotides, and the position and number of substituents in GBI-10 that were critical to the TN-C binding ability. Stabilized TN-C-binding DNA aptamers were prepared and they could be further developed for tumor imaging. Our strategy to introduce 2'-dI and d-/l-isoNA modifications after the selection process is likely to be generally applicable to improve the in vivo stability of aptamers without compromising their binding ability.
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Affiliation(s)
- Kunfeng Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Jiali Deng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Xiantao Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Xinmeng Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Liyu Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Yi Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Zhu Guan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Yun Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
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Gu F, Hu C, Xia Q, Gong C, Gao S, Chen Z. Aptamer-conjugated multi-walled carbon nanotubes as a new targeted ultrasound contrast agent for the diagnosis of prostate cancer. JOURNAL OF NANOPARTICLE RESEARCH : AN INTERDISCIPLINARY FORUM FOR NANOSCALE SCIENCE AND TECHNOLOGY 2018; 20:303. [PMID: 30524190 PMCID: PMC6244773 DOI: 10.1007/s11051-018-4407-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 10/26/2018] [Indexed: 05/09/2023]
Abstract
Early diagnosis is primarily important for the therapeutic and prognostic outcomes of malignancies including prostate cancer (PCa). However, the visuality and veracity of ultrasound imaging for the diagnosis and prognostic prediction of PCa remains poor at present. In this study, we developed a new nanoultrasound contrast agent by modifying multi-walled carbon nanotubes (MWCNTs) with polyethylene glycol (PEG) and anti-PSMA aptamer. The result showed that the modified MWCNTs offered better visuality and veracity and were able to target PCa cells more effectively as compared with the traditional contrast agent. The zeta potential was about - 38 mv. The length of this contrast agent was about 400 nm and the diameter of it was about 30 nm. The zeta potential, TEM, and FT-IR all proved the successful preparation of the agent. The vitro cytological study revealed good cell uptake and biocompatibility of the new contrast agent. The minimum detection concentration in vitro is 10 μg/ml. The earliest stage of the detection was under the parameters of frequency = 6.0 MHz and medical index = 0.06. Both in vitro and in vivo ultrasound imaging demonstrated that the new nanoultrasound contrast agent had a good development effect, distribution, and metabolism, and may prove to be a good targeted ultrasound contrast agent, especially for PCa.
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Affiliation(s)
- Fenfen Gu
- Department of Pharmacy, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, No. 1665 Kongjiang Road, Yangpu District, Shanghai, 200092 China
- Department of Pharmacy, Changhai Hospital, Second Military Medical University, No. 168 Changhai Road, Yangpu District, Shanghai, 200092 China
| | - Chuling Hu
- Department of Pharmacy, Changhai Hospital, Second Military Medical University, No. 168 Changhai Road, Yangpu District, Shanghai, 200092 China
- Department of Pharmacy, Jiaxing Maternity and Child Health Care Hospital, No. 2468, Central ring road, Jiaxing, 314000 China
| | - Qingming Xia
- Department of Pharmacy, Changhai Hospital, Second Military Medical University, No. 168 Changhai Road, Yangpu District, Shanghai, 200092 China
| | - Chunai Gong
- Department of Pharmacy, Changhai Hospital, Second Military Medical University, No. 168 Changhai Road, Yangpu District, Shanghai, 200092 China
| | - Shen Gao
- Department of Pharmacy, Changhai Hospital, Second Military Medical University, No. 168 Changhai Road, Yangpu District, Shanghai, 200092 China
| | - Zhongjian Chen
- Department of Pharmacy, Changhai Hospital, Second Military Medical University, No. 168 Changhai Road, Yangpu District, Shanghai, 200092 China
- Department of Pharmacy, Shanghai Dermatology Hospital, No. 200, Wuyi Road, Changning District, Shanghai, 200050 China
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Pi F, Binzel DW, Lee TJ, Li Z, Sun M, Rychahou P, Li H, Haque F, Wang S, Croce CM, Guo B, Evers BM, Guo P. Nanoparticle orientation to control RNA loading and ligand display on extracellular vesicles for cancer regression. NATURE NANOTECHNOLOGY 2018; 13:82-89. [PMID: 29230043 PMCID: PMC5762263 DOI: 10.1038/s41565-017-0012-z] [Citation(s) in RCA: 321] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 10/04/2017] [Indexed: 05/07/2023]
Abstract
Nanotechnology offers many benefits, and here we report an advantage of applying RNA nanotechnology for directional control. The orientation of arrow-shaped RNA was altered to control ligand display on extracellular vesicle membranes for specific cell targeting, or to regulate intracellular trafficking of small interfering RNA (siRNA) or microRNA (miRNA). Placing membrane-anchoring cholesterol at the tail of the arrow results in display of RNA aptamer or folate on the outer surface of the extracellular vesicle. In contrast, placing the cholesterol at the arrowhead results in partial loading of RNA nanoparticles into the extracellular vesicles. Taking advantage of the RNA ligand for specific targeting and extracellular vesicles for efficient membrane fusion, the resulting ligand-displaying extracellular vesicles were capable of specific delivery of siRNA to cells, and efficiently blocked tumour growth in three cancer models. Extracellular vesicles displaying an aptamer that binds to prostate-specific membrane antigen, and loaded with survivin siRNA, inhibited prostate cancer xenograft. The same extracellular vesicle instead displaying epidermal growth-factor receptor aptamer inhibited orthotopic breast cancer models. Likewise, survivin siRNA-loaded and folate-displaying extracellular vesicles inhibited patient-derived colorectal cancer xenograft.
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Affiliation(s)
- Fengmei Pi
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Daniel W Binzel
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Tae Jin Lee
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, USA
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhefeng Li
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Meiyan Sun
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA
| | - Piotr Rychahou
- Markey Cancer Center, Department of Surgery, University of Kentucky, Lexington, KY, USA
| | - Hui Li
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Farzin Haque
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Shaoying Wang
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Carlo M Croce
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Bin Guo
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA
| | - B Mark Evers
- Markey Cancer Center, Department of Surgery, University of Kentucky, Lexington, KY, USA
| | - Peixuan Guo
- College of Pharmacy, The Ohio State University, Columbus, OH, USA.
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA.
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA.
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, USA.
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Ruscito A, McConnell EM, Koudrina A, Velu R, Mattice C, Hunt V, McKeague M, DeRosa MC. In Vitro Selection and Characterization of DNA Aptamers to a Small Molecule Target. ACTA ACUST UNITED AC 2017; 9:233-268. [PMID: 29241295 DOI: 10.1002/cpch.28] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Aptamers, synthetic oligonucleotide-based molecular recognition probes, have found use in a wide array of biosensing technologies based on their tight and highly selective binding to a variety of molecular targets. However, the inherent challenges associated with the selection and characterization of aptamers for small molecule targets have resulted in their underrepresentation, despite the need for small molecule detection in fields such as medicine, the environment, and agriculture. This protocol describes the steps in the selection, sequencing, affinity characterization, and truncation of DNA aptamers that are specific for small molecule targets. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Erin M McConnell
- Chemistry Department, Carleton University, Ottawa, Ontario, Canada
| | - Anna Koudrina
- Chemistry Department, Carleton University, Ottawa, Ontario, Canada
| | - Ranganathan Velu
- Chemistry Department, Carleton University, Ottawa, Ontario, Canada
| | | | - Vernon Hunt
- Chemistry Department, Carleton University, Ottawa, Ontario, Canada
| | - Maureen McKeague
- Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
| | - Maria C DeRosa
- Chemistry Department, Carleton University, Ottawa, Ontario, Canada
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