Computational predictive approaches for interaction and structure of aptamers

Emami, Neda; Pakchin, Parvin Samadi; Ferdousi, Reza

doi:10.1016/j.jtbi.2020.110268

Cited by 25 publications

(5 citation statements)

References 146 publications

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“…Taking into account the wealth of information provided by computational studies performed in this field [147,148], this gap of information could be filled by systematically investigating the intrinsic structural/dynamics in the unbound state of the aptamers whose structure complexed with proteins is available. Studies of this type conducted on the aptamers targeting the ribosomal S8 protein [143] or NF-κB [144] demonstrated that protein-aptamer recognition may rely on different mechanisms, i.e., induced fit or population selection.…”

Section: Discussionmentioning

confidence: 99%

Structural Insights into Protein–Aptamer Recognitions Emerged from Experimental and Computational Studies

Troisi,

Balasco,

Autiero

et al. 2023

IJMS

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Aptamers are synthetic nucleic acids that are developed to target with high affinity and specificity chemical entities ranging from single ions to macromolecules and present a wide range of chemical and physical properties. Their ability to selectively bind proteins has made these compounds very attractive and versatile tools, in both basic and applied sciences, to such an extent that they are considered an appealing alternative to antibodies. Here, by exhaustively surveying the content of the Protein Data Bank (PDB), we review the structural aspects of the protein–aptamer recognition process. As a result of three decades of structural studies, we identified 144 PDB entries containing atomic-level information on protein–aptamer complexes. Interestingly, we found a remarkable increase in the number of determined structures in the last two years as a consequence of the effective application of the cryo-electron microscopy technique to these systems. In the present paper, particular attention is devoted to the articulated architectures that protein–aptamer complexes may exhibit. Moreover, the molecular mechanism of the binding process was analyzed by collecting all available information on the structural transitions that aptamers undergo, from their protein-unbound to the protein-bound state. The contribution of computational approaches in this area is also highlighted.

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Section: Discussionmentioning

confidence: 99%

Structural Insights into Protein–Aptamer Recognitions Emerged from Experimental and Computational Studies

Troisi,

Balasco,

Autiero

et al. 2023

IJMS

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show abstract

“…The design of aptamers based on their structure prediction would permit the abandonment of the SELEX process, which acts as a random selection, and the design of aptamers on demand. Furthermore, this approach would allow for the optimisation of their performance in a highly efficient manner [91]. While aptamers have been used in clinical settings to a limited extent, numerous aptamer-based clinical studies are currently underway, with the potential for their wider application in clinical practice [92].…”

Section: Implementation Of Aptamersmentioning

confidence: 99%

New Insights into Aptamers: An Alternative to Antibodies in the Detection of Molecular Biomarkers

Domsicova,

Korcekova,

Poturnayova

et al. 2024

IJMS

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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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“…These have come to solve problems of efficient and successful identification of new or high‐performance aptamers from the combinatorial library using the SELEX technology. Additionally, high cost, labor, and time further limit the SELEX process (Emami et al, 2020 ). These computational methods have revolutionized the separation and identification efficiencies; decreased amplification bias and nonspecific binding; and enabled the expansion of different base types.…”

Section: Future Perspectivementioning

confidence: 99%

Aptamers as promising nanotheranostic tools in the COVID‐19 pandemic era

Dzuvor

Tettey

Danquah

2022

WIREs Nanomed Nanobiotechnol

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The emergence of SARS‐COV‐2, the causative agent of new coronavirus disease (COVID‐19) has become a pandemic threat. Early and precise detection of the virus is vital for effective diagnosis and treatment. Various testing kits and assays, including nucleic acid detection methods, antigen tests, serological tests, and enzyme‐linked immunosorbent assay (ELISA), have been implemented or are being explored to detect the virus and/or characterize cellular and antibody responses to the infection. However, these approaches have inherent drawbacks such as nonspecificity, high cost, are characterized by long turnaround times for test results, and can be labor‐intensive. Also, the circulating SARS‐COV‐2 variant of concerns, reduced antibody sensitivity and/or neutralization, and possible antibody‐dependent enhancement (ADE) have warranted the search for alternative potent therapeutics. Aptamers, which are single‐stranded oligonucleotides, generated artificially by SELEX (Evolution of Ligands by Exponential Enrichment) may offer the capacity to generate high‐affinity neutralizers and/or bioprobes for monitoring relevant SARS‐COV‐2 and COVID‐19 biomarkers. This article reviews and discusses the prospects of implementing aptamers for rapid point‐of‐care detection and treatment of SARS‐COV‐2. We highlight other SARS‐COV‐2 targets (N protein, spike protein stem‐helix), SELEX augmented with competition assays and in silico technologies for rapid discovery and isolation of theranostic aptamers against COVID‐19 and future pandemics. It further provides an overview on site‐specific bioconjugation approaches, customizable molecular scaffolding strategies, and nanotechnology platforms to engineer these aptamers into ultrapotent blockers, multivalent therapeutics, and vaccines to boost both humoral and cellular immunity against the virus. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Diagnostic Tools > Biosensing Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease Therapeutic Approaches and Drug Discovery > Nanomedicine for Respiratory Disease

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Computational predictive approaches for interaction and structure of aptamers

Cited by 25 publications

References 146 publications

Structural Insights into Protein–Aptamer Recognitions Emerged from Experimental and Computational Studies

Structural Insights into Protein–Aptamer Recognitions Emerged from Experimental and Computational Studies

New Insights into Aptamers: An Alternative to Antibodies in the Detection of Molecular Biomarkers

Aptamers as promising nanotheranostic tools in the COVID‐19 pandemic era

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