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Alharbi M, Rhouati A, Zourob M. Selection of DNA aptamer for label-free electrochemical aptasensor for the detection of rubella virus. Talanta 2024; 278:126470. [PMID: 38996565 DOI: 10.1016/j.talanta.2024.126470] [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: 01/03/2024] [Revised: 06/18/2024] [Accepted: 06/22/2024] [Indexed: 07/14/2024]
Abstract
The Rubella virus (RUBV) is a highly contagious pathogen classified within the rubivirus genus, primarily infecting humans and transmitted via airborne routes. RUBV infection generally manifests as a mild illness reminiscent of measles. However, when affecting pregnant women, it can lead to a severe condition known as congenital rubella syndrome (CRS). Rubella infection could be also associated with joint pain, arthritis, and neurological disorders. Determination of Rubella immunity and diagnosis conventionally involve the Hemagglutination Inhibition (HI) test or the Enzyme-Linked Immunosorbent Assay (ELISA). In this study, we describe the selection and characterization of specific aptamers targeting the Rubella virus by using the process of Systematic Evolution of Ligands by EXponantial enrichment (SELEX). The Binding affinity studies have shown that the two aptamers; R-7 and R-5 display the lowest dissociation constants (Kd) of 6.58 nM and 19.05 nM, respectively. Then, R-7 aptamer was modified with a thiol group to enable its immobilization on screen-printed gold electrodes for the Rubella virus aptasensing. The label-free electrochemical detection was achieved using square wave voltammetry (SWV). The designed aptasensor has shown an excellent performance in detecting the Rubella virus within the range of 0.0005 ng/ml to 1000 ng/ml antigen and a limit of detection (LOD) of 0.00015 ng/ml. Selectivity studies were also performed against other viral antigens and serum proteins. Finally, the biosensor applicability was successfully demonstrated in spiked serum samples.
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Affiliation(s)
- Maha Alharbi
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Road, Riyadh, 11533, Saudi Arabia
| | - Amina Rhouati
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Road, Riyadh, 11533, Saudi Arabia
| | - Mohammed Zourob
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Road, Riyadh, 11533, Saudi Arabia.
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2
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Rezaee MA, Shobeiri SS, Moghadam M, Mashayekhi K, Sankian M. In vitro identification of single-stranded DNA aptamers targeting human IL-23 using the protein-SELEX strategy. J Pharm Biomed Anal 2024; 247:116245. [PMID: 38810331 DOI: 10.1016/j.jpba.2024.116245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/15/2024] [Accepted: 05/19/2024] [Indexed: 05/31/2024]
Abstract
Interleukin (IL)-23 inhibitor monoclonal antibodies shown significant efficacy in treating autoimmune diseases. DNA or RNA aptamers exhibit comparable specificity to antibodies, are cost-effective, non-immunogenic, and do not have batch to batch variation. This study aimed to characterize a single-stranded DNA (ssDNA) aptamer targeting human IL-23. The alpha subunit of IL-23 (P19) and intact IL-23 were cloned, expressed, and the proteins finally were purified through Ni2+-iminodiacetic acid affinity chromatography. The selection and characterization of ssDNA aptamer against P19 were conducted using the protein-systematic evolution of ligands by exponential enrichment (SELEX). Dot blot assay was carried out to monitor binding of the aptamer output of SELEX rounds, to P19 protein. The dissociation constant (Kd) of aptamers with positive results in dot blot assay, determined based on their binding to IL-23 using an ELISA method. Recombinant P19 and IL-23 proteins were 26 and 72 kDa, respectively, observed on SDS-PAGE .12 %. The aptamers output from 7, 8, 9, 10, 11, and 12 rounds of the SELEX was monitored by dot blot assay, revealing that the aptamer from the round 8 has stronger luminescent signal and was selected for TA-cloning. After analyzing the biotinylated aptamers from clones, positive clones in dot blot assay and ELISA were sequenced. Finally, the Kd calculation revealed three aptamers with high affinity, named A23P3, A23P6, and A23P15 with Kd values of 1.37, 2.139, and 2.88 nM, respectively. Results of this study introduced three specific anti-IL-23 ssDNA aptamers with high affinity, which could be utilized for therapeutic and diagnostic purposes.
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Affiliation(s)
- Mohammad Ali Rezaee
- Immunology Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medical Laboratory Sciences, Faculty of Paramedical, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Saeideh Sadat Shobeiri
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Malihe Moghadam
- Immunology Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Kazem Mashayekhi
- Department of Immunology, Faculty of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Mojtaba Sankian
- Immunology Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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3
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Domsicova M, Korcekova J, Poturnayova A, Breier A. New Insights into Aptamers: An Alternative to Antibodies in the Detection of Molecular Biomarkers. Int J Mol Sci 2024; 25:6833. [PMID: 38999943 PMCID: PMC11240909 DOI: 10.3390/ijms25136833] [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: 05/30/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/14/2024] Open
Abstract
Aptamers are short oligonucleotides with single-stranded regions or peptides that recently started to transform the field of diagnostics. Their unique ability to bind to specific target molecules with high affinity and specificity is at least comparable to many traditional biorecognition elements. Aptamers are synthetically produced, with a compact size that facilitates deeper tissue penetration and improved cellular targeting. Furthermore, they can be easily modified with various labels or functional groups, tailoring them for diverse applications. Even more uniquely, aptamers can be regenerated after use, making aptasensors a cost-effective and sustainable alternative compared to disposable biosensors. This review delves into the inherent properties of aptamers that make them advantageous in established diagnostic methods. Furthermore, we will examine some of the limitations of aptamers, such as the need to engage in bioinformatics procedures in order to understand the relationship between the structure of the aptamer and its binding abilities. The objective is to develop a targeted design for specific targets. We analyse the process of aptamer selection and design by exploring the current landscape of aptamer utilisation across various industries. Here, we illuminate the potential advantages and applications of aptamers in a range of diagnostic techniques, with a specific focus on quartz crystal microbalance (QCM) aptasensors and their integration into the well-established ELISA method. This review serves as a comprehensive resource, summarising the latest knowledge and applications of aptamers, particularly highlighting their potential to revolutionise diagnostic approaches.
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Affiliation(s)
- Michaela Domsicova
- Centre of Biosciences, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Dúbravská Cesta 9, 84005 Bratislava, Slovakia; (M.D.); (J.K.); (A.P.)
| | - Jana Korcekova
- Centre of Biosciences, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Dúbravská Cesta 9, 84005 Bratislava, Slovakia; (M.D.); (J.K.); (A.P.)
| | - Alexandra Poturnayova
- Centre of Biosciences, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Dúbravská Cesta 9, 84005 Bratislava, Slovakia; (M.D.); (J.K.); (A.P.)
| | - Albert Breier
- Centre of Biosciences, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Dúbravská Cesta 9, 84005 Bratislava, Slovakia; (M.D.); (J.K.); (A.P.)
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 81237 Bratislava, Slovakia
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4
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Mahjoubin-Tehran M, Rezaei S, Santos RD, Jamialahmadi T, Almahmeed W, Sahebkar A. Targeting PCSK9 as a key player in lipid metabolism: exploiting the therapeutic and biosensing potential of aptamers. Lipids Health Dis 2024; 23:156. [PMID: 38796450 PMCID: PMC11128129 DOI: 10.1186/s12944-024-02151-8] [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: 12/04/2023] [Accepted: 05/17/2024] [Indexed: 05/28/2024] Open
Abstract
The degradation of low-density lipoprotein receptor (LDLR) is induced by proprotein convertase subtilisin/kexin type 9 (PCSK9), resulting in elevated plasma concentrations of LDL cholesterol. Therefore, inhibiting the interactions between PCSK9 and LDLR is a desirable therapeutic goal for managing hypercholesterolemia. Aptamers, which are RNA or single-stranded DNA sequences, can recognize their targets based on their secondary structure. Aptamers exhibit high selectivity and affinity for binding to target molecules. The systematic evolution of ligands by exponential enrichment (SELEX), a combination of biological approaches, is used to screen most aptamers in vitro. Due to their unique advantages, aptamers have garnered significant interest since their discovery and have found extensive applications in various fields. Aptamers have been increasingly utilized in the development of biosensors for sensitive detection of pathogens, analytes, toxins, drug residues, and malignant cells. Furthermore, similar to monoclonal antibodies, aptamers can serve as therapeutic tools. Unlike certain protein therapeutics, aptamers do not elicit antibody responses, and their modified sugars at the 2'-positions generally prevent toll-like receptor-mediated innate immune responses. The focus of this review is on aptamer-based targeting of PCSK9 and the application of aptamers both as biosensors and therapeutic agents.
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Affiliation(s)
- Maryam Mahjoubin-Tehran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Samaneh Rezaei
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Raul D Santos
- Lipid Clinic Heart Institute (Incor), University of São Paulo, Medical School Hospital, São Paulo, Brazil
| | - Tannaz Jamialahmadi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Toxicology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Wael Almahmeed
- Heart and Vascular Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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Ramachandran L, Abul Rub F, Hajja A, Alodhaibi I, Arai M, Alfuwais M, Makhzoum T, Yaqinuddin A, Al-Kattan K, Assiri AM, Broering DC, Chinnappan R, Mir TA, Mani NK. Biosensing of Alpha-Fetoprotein: A Key Direction toward the Early Detection and Management of Hepatocellular Carcinoma. BIOSENSORS 2024; 14:235. [PMID: 38785709 PMCID: PMC11117836 DOI: 10.3390/bios14050235] [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: 03/18/2024] [Revised: 04/16/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
Hepatocellular carcinoma (HCC) is currently one of the most prevalent cancers worldwide. Associated risk factors include, but are not limited to, cirrhosis and underlying liver diseases, including chronic hepatitis B or C infections, excessive alcohol consumption, nonalcoholic fatty liver disease (NAFLD), and exposure to chemical carcinogens. It is crucial to detect this disease early on before it metastasizes to adjoining parts of the body, worsening the prognosis. Serum biomarkers have proven to be a more accurate diagnostic tool compared to imaging. Among various markers such as nucleic acids, circulating genetic material, proteins, enzymes, and other metabolites, alpha-fetoprotein (AFP) is a protein marker primarily used to diagnose HCC. However, current methods need a large sample and carry a high cost, among other challenges, which can be improved using biosensing technology. Early and accurate detection of AFP can prevent severe progression of the disease and ensure better management of HCC patients. This review sheds light on HCC development in the human body. Afterward, we outline various types of biosensors (optical, electrochemical, and mass-based), as well as the most relevant studies of biosensing modalities for non-invasive monitoring of AFP. The review also explains these sensing platforms, detection substrates, surface modification agents, and fluorescent probes used to develop such biosensors. Finally, the challenges and future trends in routine clinical analysis are discussed to motivate further developments.
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Affiliation(s)
- Lohit Ramachandran
- Microfluidics, Sensors and Diagnostics (μSenD) Laboratory, Centre for Microfluidics, Biomarkers, Photoceutics and Sensors (μBioPS), Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, India;
| | - Farah Abul Rub
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (F.A.R.); (A.H.); (I.A.); (M.A.); (M.A.); (T.M.); (A.Y.); (K.A.-K.); (A.M.A.); (D.C.B.)
| | - Amro Hajja
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (F.A.R.); (A.H.); (I.A.); (M.A.); (M.A.); (T.M.); (A.Y.); (K.A.-K.); (A.M.A.); (D.C.B.)
| | - Ibrahim Alodhaibi
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (F.A.R.); (A.H.); (I.A.); (M.A.); (M.A.); (T.M.); (A.Y.); (K.A.-K.); (A.M.A.); (D.C.B.)
| | - Momo Arai
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (F.A.R.); (A.H.); (I.A.); (M.A.); (M.A.); (T.M.); (A.Y.); (K.A.-K.); (A.M.A.); (D.C.B.)
| | - Mohammed Alfuwais
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (F.A.R.); (A.H.); (I.A.); (M.A.); (M.A.); (T.M.); (A.Y.); (K.A.-K.); (A.M.A.); (D.C.B.)
| | - Tariq Makhzoum
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (F.A.R.); (A.H.); (I.A.); (M.A.); (M.A.); (T.M.); (A.Y.); (K.A.-K.); (A.M.A.); (D.C.B.)
| | - Ahmed Yaqinuddin
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (F.A.R.); (A.H.); (I.A.); (M.A.); (M.A.); (T.M.); (A.Y.); (K.A.-K.); (A.M.A.); (D.C.B.)
| | - Khaled Al-Kattan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (F.A.R.); (A.H.); (I.A.); (M.A.); (M.A.); (T.M.); (A.Y.); (K.A.-K.); (A.M.A.); (D.C.B.)
- Lung Health Center Department, Organ Transplant Centre of Excellence, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Abdullah M. Assiri
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (F.A.R.); (A.H.); (I.A.); (M.A.); (M.A.); (T.M.); (A.Y.); (K.A.-K.); (A.M.A.); (D.C.B.)
- Tissue/Organ Bioengineering & BioMEMS Laboratory, Organ Transplant Centre of Excellence (TR&I-Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Dieter C. Broering
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (F.A.R.); (A.H.); (I.A.); (M.A.); (M.A.); (T.M.); (A.Y.); (K.A.-K.); (A.M.A.); (D.C.B.)
- Tissue/Organ Bioengineering & BioMEMS Laboratory, Organ Transplant Centre of Excellence (TR&I-Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Raja Chinnappan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (F.A.R.); (A.H.); (I.A.); (M.A.); (M.A.); (T.M.); (A.Y.); (K.A.-K.); (A.M.A.); (D.C.B.)
- Tissue/Organ Bioengineering & BioMEMS Laboratory, Organ Transplant Centre of Excellence (TR&I-Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Tanveer Ahmad Mir
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; (F.A.R.); (A.H.); (I.A.); (M.A.); (M.A.); (T.M.); (A.Y.); (K.A.-K.); (A.M.A.); (D.C.B.)
- Tissue/Organ Bioengineering & BioMEMS Laboratory, Organ Transplant Centre of Excellence (TR&I-Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Naresh Kumar Mani
- Microfluidics, Sensors and Diagnostics (μSenD) Laboratory, Centre for Microfluidics, Biomarkers, Photoceutics and Sensors (μBioPS), Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, India;
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6
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Liang X, He C, Shen H. Programmable stopped-flow injection analysis: A comparative study on the effects of adenosine and its aptamer on respiratory burst of salivary and circulatory neutrophils. Talanta 2024; 271:125672. [PMID: 38295446 DOI: 10.1016/j.talanta.2024.125672] [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: 09/10/2023] [Revised: 01/06/2024] [Accepted: 01/13/2024] [Indexed: 02/02/2024]
Abstract
Neutrophils play a pivotal role in innate immunity by releasing ROS through respiratory bursts to neutralize various pathogenic factors. However, excessive ROS release can cause tissue damage. Adenosine is an endogenous anti-inflammatory molecule inhibiting respiratory burst to protect the host. Adenosine aptamers with antibody-like properties and good stability are expected to act as adenosine antagonists with functional modulation capability. This study compares the effects of adenosine and its aptamer on the respiratory bursts of salivary polymorphonuclear leukocytes and circulating polymorphonuclear leukocytes using a programmable stopped-flow injection approach, ensuring rapid and efficient analysis while maintaining the neutrophils' viability. The results show that primed salivary polymorphonuclear leukocytes exhibit specificities that differ from circulating polymorphonuclear leukocytes. Adenosine aptamer can function as an inhibitory antagonist that distinguishes between physiologically controlled and excessive priming of neutrophils, showing potential application prospects in immunotherapy.
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Affiliation(s)
- Xiaoning Liang
- Institute of Analytical Chemistry, Zhejiang University 310058, China.
| | - Chaoman He
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, China; Qiantang Hospital, Hangzhou, China.
| | - Hong Shen
- Institute of Analytical Chemistry, Zhejiang University 310058, China.
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7
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Woldekidan HB, Nxumalo Z, Takundwa MM, Woldesemayat AA, Thimiri Govinda Raj DB. Protocol for Testing the Effects of ssDNA Aptamer in HeLa and MCF-7. Methods Mol Biol 2024. [PMID: 38634995 DOI: 10.1007/7651_2024_539] [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: 04/19/2024]
Abstract
Conventional approaches for treating tumors encompass chemotherapy, radiotherapy, and surgery. However, these methods come with their limitations when applied in clinical practice. Aptamers are often referred to as "chemical antibodies" and consist of short DNA or RNA molecules, designed to bind to a wide range of targets, including proteins or nucleic acid structures. They exhibit strong affinities and remarkable specificity for their target molecules, making them capable of functioning as therapeutic agents to directly impede tumor cell proliferation. This approach helps minimize the harm to normal cells, thus reducing toxicity through decreased side effects. Here we report the procedure to develop ssDNA aptamer and investigate its ability to inhibit cancer cell proliferation in HeLa and MCF-7 cancer cell lines.
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Affiliation(s)
- Haregewoin Bezu Woldekidan
- Department of Biotechnology, College of Natural and Applied Science, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
- Synthetic Nanobiotechnology and Biomachines, Synthetic Biology and Precision Medicine Centre, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Zandile Nxumalo
- Synthetic Nanobiotechnology and Biomachines, Synthetic Biology and Precision Medicine Centre, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Mutsa M Takundwa
- Synthetic Nanobiotechnology and Biomachines, Synthetic Biology and Precision Medicine Centre, Council for Scientific and Industrial Research, Pretoria, South Africa.
| | - Adugna Abdi Woldesemayat
- Department of Biotechnology, College of Natural and Applied Science, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Deepak B Thimiri Govinda Raj
- Synthetic Nanobiotechnology and Biomachines, Synthetic Biology and Precision Medicine Centre, Council for Scientific and Industrial Research, Pretoria, South Africa.
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8
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Gamboa J, Lourenço P, Cruz C, Gallardo E. Aptamers for the Delivery of Plant-Based Compounds: A Review. Pharmaceutics 2024; 16:541. [PMID: 38675202 PMCID: PMC11053555 DOI: 10.3390/pharmaceutics16040541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Natural compounds have a high potential for the treatment of various conditions, including infections, inflammatory diseases, and cancer. However, they usually present poor pharmacokinetics, low specificity, and even toxicity, which limits their use. Therefore, targeted drug delivery systems, typically composed of a carrier and a targeting ligand, can enhance natural product selectivity and effectiveness. Notably, aptamers-short RNA or single-stranded DNA molecules-have gained attention as promising ligands in targeted drug delivery since they are simple to synthesize and modify, and they present high tissue permeability, stability, and a wide array of available targets. The combination of natural products, namely plant-based compounds, with a drug delivery system utilizing aptamers as targeting agents represents an emerging strategy that has the potential to broaden its applications. This review discusses the potential of aptamers as targeting agents in the delivery of natural compounds, as well as new trends and developments in their utilization in the field of medicine.
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Affiliation(s)
- Joana Gamboa
- Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior (CICS-UBI), Av. Infante D. Henrique, 6201-506 Covilhã, Portugal; (J.G.); (P.L.)
| | - Pedro Lourenço
- Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior (CICS-UBI), Av. Infante D. Henrique, 6201-506 Covilhã, Portugal; (J.G.); (P.L.)
| | - Carla Cruz
- Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior (CICS-UBI), Av. Infante D. Henrique, 6201-506 Covilhã, Portugal; (J.G.); (P.L.)
- Departamento de Química, Faculdade de Ciências, Universidade da Beira Interior, Rua Marquês de Ávila e Bolama, 6201-001 Covilhã, Portugal
| | - Eugenia Gallardo
- Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior (CICS-UBI), Av. Infante D. Henrique, 6201-506 Covilhã, Portugal; (J.G.); (P.L.)
- Laboratório de Fármaco-Toxicologia, UBIMedical, Universidade da Beira Interior, EM506, 6200-000 Covilhã, Portugal
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Mahmoudian F, Ahmari A, Shabani S, Sadeghi B, Fahimirad S, Fattahi F. Aptamers as an approach to targeted cancer therapy. Cancer Cell Int 2024; 24:108. [PMID: 38493153 PMCID: PMC10943855 DOI: 10.1186/s12935-024-03295-4] [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: 11/28/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
Conventional cancer treatments can cause serious side effects because they are not specific to cancer cells and can damage healthy cells. Aptamers often are single-stranded oligonucleotides arranged in a unique architecture, allowing them to bind specifically to target sites. This feature makes them an ideal choice for targeted therapeutics. They are typically produced through the systematic evolution of ligands by exponential enrichment (SELEX) and undergo extensive pharmacological revision to modify their affinity, specificity, and therapeutic half-life. Aptamers can act as drugs themselves, directly inhibiting tumor cells. Alternatively, they can be used in targeted drug delivery systems to transport drugs directly to tumor cells, minimizing toxicity to healthy cells. In this review, we will discuss the latest and most advanced approaches to using aptamers for cancer treatment, particularly targeted therapy overcoming resistance to conventional therapies.
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Affiliation(s)
- Fatemeh Mahmoudian
- Cancer Research Center, Semnan University of Medical Sciences, Semnan, Iran
- Clinical Research Development Unit of Ayatollah-Khansari Hospital, Arak University of Medical Sciences, Arak, Iran
| | - Azin Ahmari
- Clinical Research Development Unit of Ayatollah-Khansari Hospital, Arak University of Medical Sciences, Arak, Iran
- Department of Radiation Oncology, School of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Shiva Shabani
- Clinical Research Development Unit of Ayatollah-Khansari Hospital, Arak University of Medical Sciences, Arak, Iran
- Department of Infectious Diseases, School of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Bahman Sadeghi
- Clinical Research Development Unit of Ayatollah-Khansari Hospital, Arak University of Medical Sciences, Arak, Iran
- Department of Community Medicine, School of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Shohreh Fahimirad
- Molecular and Medicine Research Center, Arak University of Medical Sciences, Arak, Iran.
| | - Fahimeh Fattahi
- Clinical Research Development Unit of Ayatollah-Khansari Hospital, Arak University of Medical Sciences, Arak, Iran.
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran.
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Wang B, Kobeissy F, Golpich M, Cai G, Li X, Abedi R, Haskins W, Tan W, Benner SA, Wang KKW. Aptamer Technologies in Neuroscience, Neuro-Diagnostics and Neuro-Medicine Development. Molecules 2024; 29:1124. [PMID: 38474636 DOI: 10.3390/molecules29051124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/15/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Aptamers developed using in vitro Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technology are single-stranded nucleic acids 10-100 nucleotides in length. Their targets, often with specificity and high affinity, range from ions and small molecules to proteins and other biological molecules as well as larger systems, including cells, tissues, and animals. Aptamers often rival conventional antibodies with improved performance, due to aptamers' unique biophysical and biochemical properties, including small size, synthetic accessibility, facile modification, low production cost, and low immunogenicity. Therefore, there is sustained interest in engineering and adapting aptamers for many applications, including diagnostics and therapeutics. Recently, aptamers have shown promise as early diagnostic biomarkers and in precision medicine for neurodegenerative and neurological diseases. Here, we critically review neuro-targeting aptamers and their potential applications in neuroscience research, neuro-diagnostics, and neuro-medicine. We also discuss challenges that must be overcome, including delivery across the blood-brain barrier, increased affinity, and improved in vivo stability and in vivo pharmacokinetic properties.
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Affiliation(s)
- Bang Wang
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
- The Foundation for Applied Molecular Evolution, 1501 NW 68th Terrace, Gainesville, FL 32605, USA
| | - Firas Kobeissy
- Center for Neurotrauma, MultiOmics and Biomarkers (CNMB), Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
- Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
- Brain Rehabilitation Research Center, Malcom Randall VA Medical Center, North Florida/South Georgia Veterans Health System, 1601 SW Archer Road, Gainesville, FL 32608, USA
- Center for Visual and Neurocognitive Rehabilitation (CVNR), Atlanta VA Health Care System, 1670 Clairmont Rd, Decatur, GA 30033, USA
| | - Mojtaba Golpich
- Center for Neurotrauma, MultiOmics and Biomarkers (CNMB), Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Guangzheng Cai
- Center for Neurotrauma, MultiOmics and Biomarkers (CNMB), Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Xiaowei Li
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Reem Abedi
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107-2020, Lebanon
| | - William Haskins
- Gryphon Bio, Inc., 611 Gateway Blvd. Suite 120 #253, South San Francisco, CA 94080, USA
| | - Weihong Tan
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences, Hangzhou 310022, China
| | - Steven A Benner
- The Foundation for Applied Molecular Evolution, 1501 NW 68th Terrace, Gainesville, FL 32605, USA
| | - Kevin K W Wang
- Center for Neurotrauma, MultiOmics and Biomarkers (CNMB), Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
- Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
- Brain Rehabilitation Research Center, Malcom Randall VA Medical Center, North Florida/South Georgia Veterans Health System, 1601 SW Archer Road, Gainesville, FL 32608, USA
- Center for Visual and Neurocognitive Rehabilitation (CVNR), Atlanta VA Health Care System, 1670 Clairmont Rd, Decatur, GA 30033, USA
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11
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Sousa AM, Ferreira D, Rodrigues LR, Pereira MO. Aptamer-based therapy for fighting biofilm-associated infections. J Control Release 2024; 367:522-539. [PMID: 38295992 DOI: 10.1016/j.jconrel.2024.01.061] [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: 09/30/2023] [Revised: 01/06/2024] [Accepted: 01/27/2024] [Indexed: 02/06/2024]
Abstract
Biofilms are key players in the pathogenesis of most of chronic infections associated with host tissue or fluids and indwelling medical devices. These chronic infections are hard to be treated due to the increased biofilms tolerance towards antibiotics in comparison to planktonic (or free living) cells. Despite the advanced understanding of their formation and physiology, biofilms continue to be a challenge and there is no standardized therapeutic approach in clinical practice to eradicate them. Aptamers offer distinctive properties, including excellent affinity, selectivity, stability, making them valuable tools for therapeutic purposes. This review explores the flexibility and designability of aptamers as antibiofilm drugs but, importantly, as targeting tools for diverse drug and delivery systems. It highlights specific examples of application of aptamers in biofilms of diverse species according to different modes of action including inhibition of motility and adhesion, blocking of quorum sensing molecules, and dispersal of biofilm-cells to planktonic state. Moreover, it discusses the limitations and challenges that impaired an increased success of the use of aptamers on biofilm management, as well as the opportunities related to aptamers modifications that can significantly expand their applicability on the biofilm field.
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Affiliation(s)
- Ana Margarida Sousa
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga, Guimarães, Portugal.
| | - Débora Ferreira
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga, Guimarães, Portugal
| | - Lígia Raquel Rodrigues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga, Guimarães, Portugal
| | - Maria Olívia Pereira
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga, Guimarães, Portugal.
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12
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Costanzo H, Gooch J, Tungsirisurp S, Frascione N. The Development and Characterisation of ssDNA Aptamers via a Modified Cell-SELEX Methodology for the Detection of Human Red Blood Cells. Int J Mol Sci 2024; 25:1814. [PMID: 38339091 PMCID: PMC10855528 DOI: 10.3390/ijms25031814] [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: 12/11/2023] [Revised: 01/25/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Blood is one of the most commonly found biological fluids at crime scenes, with the detection and identification of blood holding a high degree of evidential value. It can provide not only information about the nature of the crime but can also lead to identification via DNA profiling. Presumptive tests for blood are usually sensitive but not specific, so small amounts of the substrate can be detected, but false-positive results are often encountered, which can be misleading. Novel methods for the detection of red blood cells based on aptamer-target interactions may be able to overcome these issues. Aptamers are single-stranded DNA or RNA sequences capable of undergoing selective antigen association due to three-dimensional structure formation. The use of aptamers as a target-specific moiety poses several advantages and has the potential to replace antibodies within immunoassays. Aptamers are cheaper to produce, display no batch-to-batch variation and can allow for a wide range of chemical modifications. They can help limit cross-reactivity, which is a hindrance to current forensic testing methods. Within this study, a modified Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process was used to generate aptamers against whole red blood cells. Obtained aptamer pools were analysed via massively parallel sequencing to identify viable sequences that demonstrate a high affinity for the target. Using bioinformatics platforms, aptamer candidates were identified via their enrichment profiles. Binding characterisation was also conducted on two selected aptamer candidates via fluorescent microscopy and qPCR to visualise and quantify aptamer binding. The potential for these aptamers is broad as they can be utilised within a range of bioassays for not only forensic applications but also other analytical science and medical applications. Potential future work includes the incorporation of developed aptamers into a biosensing platform that can be used at crime scenes for the real-time detection of human blood.
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Affiliation(s)
| | | | | | - Nunzianda Frascione
- Department of Analytical, Environmental & Forensic Sciences, Faculty of Life Sciences & Medicine, King’s College London, London SE1 9NH, UK; (H.C.); (J.G.); (S.T.)
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13
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Ma Z, Chen H, Yang Y, Gao S, Yang J, Cui S, Zhou S, Jiang B, Zou B, Sun M, Wang L. Characterization of an ssDNA ligase and its application in aptamer circularization. Anal Biochem 2024; 685:115409. [PMID: 38006953 DOI: 10.1016/j.ab.2023.115409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/08/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Aptamers are widely used in various biomedical areas as novel molecular recognition elements, however, short single-stranded DNA (ssDNA) or RNA oligonucleotides are easily degraded by nucleases in biological fluids. This problem can be solved by circularizing aptamers with circular ligases. Herein, a moderately thermostable ssDNA ligase was expressed and purified. The purified ligase showed good circularization activity for different length substrates and much higher circularization efficiency than T4 RNA ligase 1. Biochemical characterization revealed that the enzyme showed optimal circularization activity at pH 7.5 and 50 ᵒC. Mn2+ and Mg2+ increased enzyme circularization activity, with Mn2+ having higher activity than Mg2+. The optimal concentrations of Mn2+ and ligase were 1.25-2.5 mM and 0.02 nM, respectively. The kinetic parameters Km, Vmax and Kcat of ssDNA ligase were 1.16 μM, 10.71 μM/min, and 10.7 min-1, respectively. The ssDNA ligase efficiency was nucleotide-dependent, and 5'-G and 3'-T were the most ligase-favored terminal nucleotides. In addition, the affinity and stability of the circular aptamer were determined. The affinity constant (KD) was 4.9 μM, and the stability increased compared to its linear form. Molecular docking results showed that the circular aptamer bound to the target via two hydrogen bonds. This study provides a simple and efficient aptamer circularization modification method for improving aptamer stability and expanding its applications.
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Affiliation(s)
- Zhenxia Ma
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China
| | - Han Chen
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China
| | - Yao Yang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China
| | - Siyi Gao
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China
| | - Jiaping Yang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China
| | - Shihai Cui
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China
| | - Shiyuan Zhou
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China
| | - Boyang Jiang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China
| | - Bin Zou
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China
| | - Mingjuan Sun
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China.
| | - Lianghua Wang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China.
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14
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Park JY, Cho YL, Chae JR, Lee JH, Kang WJ. Enhancement of in vivo targeting properties of ErbB2 aptamer by chemical modification. PLoS One 2023; 18:e0291624. [PMID: 37729138 PMCID: PMC10511116 DOI: 10.1371/journal.pone.0291624] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/04/2023] [Indexed: 09/22/2023] Open
Abstract
Aptamers have great potential for diagnostics and therapeutics due to high specificity to target molecules. However, studies have shown that aptamers are rapidly distributed and excreted from blood circulation due to nuclease degradation. To overcome this issue and to improve in vivo pharmacokinetic properties, inverted deoxythymidine (idT) incorporation at the end of aptamer has been developed. The goal of this study was to evaluate the biological characterization of 3'-idT modified ErbB2 aptamer and compare with that of unmodified aptamer via nuclear imaging. ErbB2-idT aptamer was labeled with radioisotope F-18 by base-pair hybridization using complementary oligonucleotide platform. The hyErbB2-idT aptamer demonstrated specific binding to targets in a ErbB2 expressing SK-BR-3 and KPL4 cells in vitro. Ex vivo biodistribution and in vivo imaging was studied in KPL4 xenograft bearing Balb/c nu/nu mice. 18F-hyErbB2-idT aptamer had significantly higher retention in the tumor (1.36 ± 0.17%ID/g) than unmodified 18F-hyErbB2 (0.98 ± 0.19%ID/g) or scrambled aptamer (0.79 ± 0.26% ID/g) at 1 h post-injection. 18F-hyErbB2-idT aptamer exhibited relatively slow blood clearance and delayed excretion by the renal and hepatobiliary system than 18F-hyErbB2 aptamer. In vivo PET imaging study showed that 18F-hyErbB2-idT aptamer had more stronger PET signals on KPL4 tumor than 18F-hyErbB2 aptamer. The results of this study demonstrate that attachment of idT at 3'-end of aptamer have a substantial influence on biological stability and extended blood circulation led to enhanced tumor uptake of aptamer.
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Affiliation(s)
- Jun Young Park
- Department of Nuclear Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ye Lim Cho
- Department of Nuclear Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ju Ri Chae
- Department of Nuclear Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung Hwan Lee
- INTEROligo Corporation, Anyang-si, Gyeonggi-do, Republic of Korea
| | - Won Jun Kang
- Department of Nuclear Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
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15
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Ruiz-Ciancio D, Lin LH, Veeramani S, Barros MN, Sanchez D, Di Bartolo AL, Masone D, Giangrande PH, Mestre MB, Thiel WH. Selection of a novel cell-internalizing RNA aptamer specific for CD22 antigen in B cell acute lymphoblastic leukemia. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:698-712. [PMID: 37662970 PMCID: PMC10469072 DOI: 10.1016/j.omtn.2023.07.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 07/25/2023] [Indexed: 09/05/2023]
Abstract
Despite improvements in B cell acute lymphoblastic leukemia (B-ALL) treatment, a significant number of patients experience relapse of the disease, resulting in poor prognosis and high mortality. One of the drawbacks of current B-ALL treatments is the high toxicity associated with the non-specificity of chemotherapeutic drugs. Targeted therapy is an appealing strategy to treat B-ALL to mitigate these toxic off-target effects. One such target is the B cell surface protein CD22. The restricted expression of CD22 on the B-cell lineage and its ligand-induced internalizing properties make it an attractive target in cases of B cell malignancies. To target B-ALL and the CD22 protein, we performed cell internalization SELEX (Systematic Evolution of Ligands by EXponential enrichment) followed by molecular docking to identify internalizing aptamers specific for B-ALL cells that bind the CD22 cell-surface receptor. We identified two RNA aptamers, B-ALL1 and B-ALL2, that target human malignant B cells, with B-ALL1 the first documented RNA aptamer interacting with the CD22 antigen. These B-ALL-specific aptamers represent an important first step toward developing novel targeted therapies for B cell malignancy treatments.
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Affiliation(s)
- Dario Ruiz-Ciancio
- Instituto de Ciencias Biomédicas (ICBM), Facultad de Ciencias Médicas, Universidad Católica de Cuyo, Av. José Ignacio de la Roza 1516, Rivadavia, San Juan 5400, Argentina
- National Council of Scientific and Technical Research (CONICET), Godoy Cruz 2290, Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
| | - Li-Hsien Lin
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52246, USA
| | - Suresh Veeramani
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52246, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA
| | - Maya N. Barros
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52246, USA
| | - Diego Sanchez
- Instituto de Medicina y Biología Experimental de Cuyo (IMBECU), CONICET, CCT-Mendoza 5500, Argentina
| | - Ary Lautaro Di Bartolo
- Instituto de Histología y Embriología de Mendoza (IHEM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), Mendoza M5502JMA, Argentina
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), Mendoza M5502JMA, Argentina
| | - Paloma H. Giangrande
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52246, USA
- VP Platform Discovery Sciences, Biology, Wave Life Sciences, 733 Concord Avenue, Cambridge, MA 02138, USA
| | - María Belén Mestre
- Instituto de Ciencias Biomédicas (ICBM), Facultad de Ciencias Médicas, Universidad Católica de Cuyo, Av. José Ignacio de la Roza 1516, Rivadavia, San Juan 5400, Argentina
- National Council of Scientific and Technical Research (CONICET), Godoy Cruz 2290, Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
| | - William H. Thiel
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52246, USA
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16
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Kong AHY, Wu AJ, Ho OKY, Leung MMK, Huang AS, Yu Y, Zhang G, Lyu A, Li M, Cheung KH. Exploring the Potential of Aptamers in Targeting Neuroinflammation and Neurodegenerative Disorders: Opportunities and Challenges. Int J Mol Sci 2023; 24:11780. [PMID: 37511539 PMCID: PMC10380291 DOI: 10.3390/ijms241411780] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Neuroinflammation is the precursor for several neurodegenerative diseases (NDDs), such as Alzheimer's disease (AD), Parkinson's disease (PD), and multiple sclerosis (MS). Targeting neuroinflammation has emerged as a promising strategy to address a wide range of CNS pathologies. These NDDs still present significant challenges in terms of limited and ineffective diagnosis and treatment options, driving the need to explore innovative and novel therapeutic alternatives. Aptamers are single-stranded nucleic acids that offer the potential for addressing these challenges through diagnostic and therapeutic applications. In this review, we summarize diagnostic and therapeutic aptamers for inflammatory biomolecules, as well as the inflammatory cells in NDDs. We also discussed the potential of short nucleotides for Aptamer-Based Targeted Brain Delivery through their unique features and modifications, as well as their ability to penetrate the blood-brain barrier. Moreover, the unprecedented opportunities and substantial challenges of using aptamers as therapeutic agents, such as drug efficacy, safety considerations, and pharmacokinetics, are also discussed. Taken together, this review assesses the potential of aptamers as a pioneering approach for target delivery to the CNS and the treatment of neuroinflammation and NDDs.
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Affiliation(s)
- Anna Hau-Yee Kong
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Aston Jiaxi Wu
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Olivia Ka-Yi Ho
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Maggie Ming-Ki Leung
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Alexis Shiying Huang
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, 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 SAR, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong SAR, 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 SAR, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong SAR, China
| | - Aiping Lyu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong SAR, China
| | - Min Li
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - King-Ho Cheung
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
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17
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Lu S, Fowler CR, Ream B, Waugh SM, Russell TM, Rohloff JC, Gold L, Cleveland JP, Stoll S. Magnetically Detected Protein Binding Using Spin-Labeled Slow Off-Rate Modified Aptamers. ACS Sens 2023; 8:2219-2227. [PMID: 37300508 DOI: 10.1021/acssensors.3c00112] [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] [Indexed: 06/12/2023]
Abstract
Recent developments in aptamer chemistry open up opportunities for new tools for protein biosensing. In this work, we present an approach to use immobilized slow off-rate modified aptamers (SOMAmers) site-specifically labeled with a nitroxide radical via azide-alkyne click chemistry as a means for detecting protein binding. Protein binding induces a change in rotational mobility of the spin label, which is detected via solution-state electron paramagnetic resonance (EPR) spectroscopy. We demonstrate the workflow and test the protocol using the SOMAmer SL5 and its protein target, platelet-derived growth factor B (PDGF-BB). In a complete site scan of the nitroxide over the SOMAmer, we determine the rotational mobility of the spin label in the absence and presence of target protein. Several sites with sufficiently tight affinity and large rotational mobility change upon protein binding are identified. We then model a system where the spin-labeled SOMAmer assay is combined with fluorescence detection via diamond nitrogen-vacancy (NV) center relaxometry. The NV center spin-lattice relaxation time is modulated by the rotational mobility of a proximal spin label and thus responsive to SOMAmer-protein binding. The spin label-mediated assay provides a general approach for transducing protein binding events into magnetically detectable signals.
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Affiliation(s)
- Shutian Lu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | | | - Brian Ream
- SomaLogic, Boulder, Colorado 80301, United States
| | | | | | | | - Larry Gold
- SomaLogic, Boulder, Colorado 80301, United States
| | | | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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18
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Ratajczak K, Stobiecka M. DNA Aptamer Beacon Probe (ABP) for Monitoring of Adenosine Triphosphate Level in SW480 Cancer Cells Treated with Glycolysis Inhibitor 2-Deoxyglucose. Int J Mol Sci 2023; 24:ijms24119295. [PMID: 37298245 DOI: 10.3390/ijms24119295] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/20/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Early cancer screening enables timely detection of carcinogenesis, and aids in prompt clinical intervention. Herein, we report on the development of a simple, sensitive, and rapid fluorometric assay based on the aptamer probe (aptamer beacon probe, ABP) for monitoring the energy-demand biomarker adenosine triphosphate (ATP), an essential energy source that is released into the tumor microenvironment. Its level plays a significant role in risk assessment of malignancies. The operation of the ABP for ATP was examined using solutions of ATP and other nucleotides (UTP, GTP, CTP), followed by monitoring of ATP production in SW480 cancer cells. Then, the effect of a glycolysis inhibitor, 2-deoxyglucose (2-DG), on SW480 cells was investigated. The stability of predominant ABP conformations in the temperature range of 23-91 °C and the effects of temperature on ABP interactions with ATP, UTP, GTP, and CTP were evaluated based on quenching efficiencies (QE) and Stern-Volmer constants (KSV). The optimized temperature for best selectivity of ABP toward ATP was 40 °C (KSV = 1093 M-1, QE = 42%). We have found that the inhibition of glycolysis in SW480 cancer cells by 2-deoxyglucose resulted in lowering of ATP production by 31.7%. Therefore, monitoring and modulation of ATP concentration may aid in future cancer treatment.
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Affiliation(s)
- Katarzyna Ratajczak
- Department of Physics and Biophysics, Warsaw University of Life Sciences, 159 Nowoursynowska Street, 02776 Warsaw, Poland
| | - Magdalena Stobiecka
- Department of Physics and Biophysics, Warsaw University of Life Sciences, 159 Nowoursynowska Street, 02776 Warsaw, Poland
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19
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Zamay T, Zamay S, Luzan N, Fedotovskaya V, Masyugin A, Zelenov F, Koshmanova A, Nikolaeva E, Kirichenko D, Veprintsev D, Kolovskaya O, Shchugoreva I, Zamay G, Lapin I, Lukyanenko A, Borus A, Sukhachev A, Volochaev M, Lukyanenko K, Shabanov A, Zabluda V, Zhizhchenko A, Kuchmizhak A, Sokolov A, Narodov A, Prokopenko V, Galeev R, Svetlichnyi V, Kichkailo A. Magnetic Nanoscalpel for the Effective Treatment of Ascites Tumors. J Funct Biomater 2023; 14:jfb14040179. [PMID: 37103269 PMCID: PMC10145876 DOI: 10.3390/jfb14040179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/16/2023] [Accepted: 03/22/2023] [Indexed: 04/28/2023] Open
Abstract
One of the promising novel methods for radical tumor resection at a single-cell level is magneto-mechanical microsurgery (MMM) with magnetic nano- or microdisks modified with cancer-recognizing molecules. A low-frequency alternating magnetic field (AMF) remotely drives and controls the procedure. Here, we present characterization and application of magnetic nanodisks (MNDs) as a surgical instrument ("smart nanoscalpel") at a single-cell level. MNDs with a quasi-dipole three-layer structure (Au/Ni/Au) and DNA aptamer AS42 (AS42-MNDs) on the surface converted magnetic moment into mechanical and destroyed tumor cells. The effectiveness of MMM was analyzed on Ehrlich ascites carcinoma (EAC) cells in vitro and in vivo using sine and square-shaped AMF with frequencies from 1 to 50 Hz with 0.1 to 1 duty-cycle parameters. MMM with the "Nanoscalpel" in a sine-shaped 20 Hz AMF, a rectangular-shaped 10 Hz AMF, and a 0.5 duty cycle was the most effective. A sine-shaped field caused apoptosis, whereas a rectangular-shaped field caused necrosis. Four sessions of MMM with AS42-MNDs significantly reduced the number of cells in the tumor. In contrast, ascites tumors continued to grow in groups of mice and mice treated with MNDs with nonspecific oligonucleotide NO-MND. Thus, applying a "smart nanoscalpel" is practical for the microsurgery of malignant neoplasms.
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Affiliation(s)
- Tatiana Zamay
- Federal Research Center "Krasnoyarsk Science Center" of the Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Sergey Zamay
- Federal Research Center "Krasnoyarsk Science Center" of the Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
| | - Natalia Luzan
- Federal Research Center "Krasnoyarsk Science Center" of the Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Victoriya Fedotovskaya
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | | | | | - Anastasia Koshmanova
- Federal Research Center "Krasnoyarsk Science Center" of the Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Elena Nikolaeva
- Federal Research Center "Krasnoyarsk Science Center" of the Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Daria Kirichenko
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Dmitry Veprintsev
- Federal Research Center "Krasnoyarsk Science Center" of the Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
| | - Olga Kolovskaya
- Federal Research Center "Krasnoyarsk Science Center" of the Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Irina Shchugoreva
- Federal Research Center "Krasnoyarsk Science Center" of the Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Galina Zamay
- Federal Research Center "Krasnoyarsk Science Center" of the Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Ivan Lapin
- Laboratory of Advanced Materials and Technology, Siberian Physical Technical Institute, Tomsk State University, Tomsk 634050, Russia
| | - Anna Lukyanenko
- L.V. Kirensky Institute of Physics, Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk 660036, Russia
| | - Andrey Borus
- L.V. Kirensky Institute of Physics, Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk 660036, Russia
| | - Alexander Sukhachev
- L.V. Kirensky Institute of Physics, Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk 660036, Russia
| | - Mikhail Volochaev
- L.V. Kirensky Institute of Physics, Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk 660036, Russia
| | - Kirill Lukyanenko
- Federal Research Center "Krasnoyarsk Science Center" of the Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Alexandr Shabanov
- Federal Research Center "Krasnoyarsk Science Center" of the Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
| | - Vladimir Zabluda
- L.V. Kirensky Institute of Physics, Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk 660036, Russia
| | - Alexey Zhizhchenko
- Institute of Automation and Control Processes (IACP), Far Eastern Branch of the Russian Academy of Science, Vladivostok 690041, Russia
- Far Eastern Federal University, Vladivostok 690950, Russia
| | - Aleksandr Kuchmizhak
- Institute of Automation and Control Processes (IACP), Far Eastern Branch of the Russian Academy of Science, Vladivostok 690041, Russia
- Far Eastern Federal University, Vladivostok 690950, Russia
| | - Alexey Sokolov
- L.V. Kirensky Institute of Physics, Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk 660036, Russia
| | - Andrey Narodov
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Vladimir Prokopenko
- V.P. Astafiev Krasnoyarsk State Pedagogical University, Krasnoyarsk 660049, Russia
| | - Rinat Galeev
- JSC «NPP «Radiosviaz», Krasnoyarsk 660021, Russia
| | - Valery Svetlichnyi
- Laboratory of Advanced Materials and Technology, Siberian Physical Technical Institute, Tomsk State University, Tomsk 634050, Russia
| | - Anna Kichkailo
- Federal Research Center "Krasnoyarsk Science Center" of the Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
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20
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Paramithiotis S. Molecular Targets for Foodborne Pathogenic Bacteria Detection. Pathogens 2023; 12:pathogens12010104. [PMID: 36678453 PMCID: PMC9865778 DOI: 10.3390/pathogens12010104] [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: 11/30/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The detection of foodborne pathogenic bacteria currently relies on their ability to grow on chemically defined liquid and solid media, which is the essence of the classical microbiological approach. Such procedures are time-consuming and the quality of the result is affected by the selectivity of the media employed. Several alternative strategies based on the detection of molecular markers have been proposed. These markers may be cell constituents, may reside on the cell envelope or may be specific metabolites. Each marker provides specific advantages and, at the same time, suffers from specific limitations. The food matrix and chemical composition, as well as the accompanying microbiota, may also severely compromise detection. The aim of the present review article is to present and critically discuss all available information regarding the molecular targets that have been employed as markers for the detection of foodborne pathogens. Their strengths and limitations, as well as the proposed alleviation strategies, are presented, with particular emphasis on their applicability in real food systems and the challenges that are yet to be effectively addressed.
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Affiliation(s)
- Spiros Paramithiotis
- Laboratory of Food Process Engineering, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
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21
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de Melo MIA, da Silva Cunha P, Ferreira IM, de Andrade ASR. DNA aptamers selection for Staphylococcus aureus cells by SELEX and Cell-SELEX. Mol Biol Rep 2023; 50:157-165. [PMID: 36315328 DOI: 10.1007/s11033-022-07991-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Staphylococcus aureus is the most common bacteria found in skin, soft tissues, bone, and bone prostheses infections. The aim of this study was to select DNA aptamers for S. aureus to be applied in the diagnosis of bacteria. METHODS AND RESULTS We used SELEX (Systematic Evolution of Ligands by EXponencial Enrichment) for peptidoglycan followed by cell-SELEX with S. aureus cells as target. Four sequences showed significantly higher binding to S. aureus distinguishing it from the control cells of other significant microbial species: Escherichia coli, Candida albicans, Streptococcus pyogenes and Streptococcus pneumoniae. In particular, ApSA1 (Kd = 62.7 ± 5.6 nM) and ApSA3 (Kd = 43.3 ± 3.0 nM) sequences combined high affinity and specificity for S. aureus, considering all microorganisms tested. CONCLUSIONS Our results demonstrated that these aptamers were able to identify peptidoglycan in the S. aureus surface and have great potential for use in the development of radiopharmaceuticals capable to identify S. aureus infectious foci, as well as in other aptamer-based methodologies for bacteria diagnosis.
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Affiliation(s)
| | - Pricila da Silva Cunha
- Centro de Desenvolvimento da Tecnologia Nuclear, CDTN, 31270-901, Belo Horizonte, MG, Brazil.,Instituto Federal de Educação, Ciência e Tecnologia do Sudeste de Minas Gerais, 36884-036, Muriaé, MG, Brazil
| | - Iêda Mendes Ferreira
- Centro de Desenvolvimento da Tecnologia Nuclear, CDTN, 31270-901, Belo Horizonte, MG, Brazil
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22
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Dhanya CR, Mary AS, Madhavan M. Aptamer-siRNA chimeras: Promising tools for targeting HER2 signaling in cancer. Chem Biol Drug Des 2022; 101:1162-1180. [PMID: 36099164 DOI: 10.1111/cbdd.14143] [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: 12/19/2021] [Revised: 08/28/2022] [Accepted: 09/11/2022] [Indexed: 11/30/2022]
Abstract
RNA interference is a transformative approach and has great potential in the development of novel and more efficient cancer therapeutics. Immense prospects exist in the silencing of HER2 and its downstream genes which are overexpressed in many cancers, through exogenously delivered siRNA. However, there is still a long way to exploit the full potential and versatility of siRNA therapeutics due to the challenges associated with the stability and delivery of siRNA targeted to specific sites. Aptamers offer several advantages as a vehicle for siRNA delivery, over other carriers such as antibodies. In this review, we discuss the progress made in the development and applications of aptamer-siRNA chimeras in HER2 targeting and gene silencing. A schematic workflow is also provided which will provide ample insight for all those researchers who are new to this field. Also, we think that a mechanistic understanding of the HER2 signaling pathway is crucial in designing extensive investigations aimed at the silencing of a wider array of genes. This review is expected to stimulate more research on aptamer-siRNA chimeras targeted against HER2 which might arm us with potential effective therapeutic interventions for the management of cancer.
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Affiliation(s)
- C R Dhanya
- Department of Biochemistry, Government College Kariavattom, Thiruvananthapuram, Kerala, India
| | - Aarcha Shanmugha Mary
- Department of Microbiology, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | - Maya Madhavan
- Department of Biochemistry, Government College for Women, Thiruvananthapuram, Kerala, India
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23
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Novel Design of RNA Aptamers as Cancer Inhibitors and Diagnosis Targeting the Tyrosine Kinase Domain of the NT-3 Growth Factor Receptor Using a Computational Sequence-Based Approach. Molecules 2022; 27:molecules27144518. [PMID: 35889390 PMCID: PMC9320020 DOI: 10.3390/molecules27144518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 12/10/2022] Open
Abstract
Aptamers, the nucleic acid analogs of antibodies, bind to their target molecules with remarkable specificity and sensitivity, making them promising diagnostic and therapeutic tools. The systematic evolution of ligands by exponential enrichment (SELEX) is time-consuming and expensive. However, regardless of those issues, it is the most used in vitro method for selecting aptamers. Therefore, recent studies have used computational approaches to reduce the time and cost associated with the synthesis and selection of aptamers. In an effort to present the potential of computational techniques in aptamer selection, a simple sequence-based method was used to design a 69-nucleotide long aptamer (mod_09) with a relatively stable structure (with a minimum free energy of −32.2 kcal/mol) and investigate its binding properties to the tyrosine kinase domain of the NT-3 growth factor receptor, for the first time, by employing computational modeling and docking tools.
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