ArticleProceedings of the National Academy of Sciences of the United States of America2020
In silico design and validation of high-affinity RNA aptamers targeting epithelial cellular adhesion molecule dimers.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 81 citations in OpenAlex.
- Article
- SELEX-Based Aptamer Technologies for Toxin Analysis: Screening, Optimization, and Computational Assisted Design.Toxins · 2026Review
- A Multi-Engine Consensus Docking Pipeline for RNA Aptamer Screening Against ACC Oxidase (ACO): Statistical Validation, Machine Learning Analysis, and Pilot Cross-Target Evaluation Against ACC Synthase (ACS).International journal of molecular sciences · 2026Article
- Aptamer-Functionalized Nanocarriers for Bone and Joint Diseases: Engineering Design Rules and Translational Roadmap.Small science · 2026Article
- In Silico Study of Anti-CD40 DNA Aptamers as Vaccine Adjuvants for Chickens.International journal of molecular sciences · 2026Article
- Advances in aptamer technology for target-based drug discovery.Journal of pharmaceutical analysis · 2026Review
- PANTHER Score: Protein-Affinity for Nucleic Target-binding, Hybridization, and Energy Regression.RNA (New York, N.Y.) · 2026Article
- Review
- Aptamers as Potential Inhibitors of Ethylene Biosynthesis: Identification and In Silico Selection.International journal of molecular sciences · 2025Article
- RNA aptamer-mediated RNA nanotechnology for potential treatment of cardiopulmonary diseases.Pharmacological research · 2025Review
- Subcellular Organelle Targeting as a Novel Approach to Combat Tumor Metastasis.Pharmaceutics · 2025Review
- Mutagenesis-based optimal design of plant peptide phytosulfokine for enhanced biological activity.Computational and structural biotechnology journal · 2025Article
- In Silico Design of Novel EpCAM-Binding Aptamers for Targeted Delivery of RNA Therapeutics.Nanomaterials (Basel, Switzerland) · 2024Article
- Review
- Inhibition of DEF-p65 Interactions as a Potential Avenue to Suppress Tumor Growth in Pancreatic Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- The Deinococcus protease PprI senses DNA damage by directly interacting with single-stranded DNA.Nature communications · 2024Article
- MultiplexedNucleic acid therapeutics · 2024Article
- In Silico Approaches for the Identification of Aptamer Binding Interactions toTropical medicine and infectious disease · 2023Article
- Design and Prediction of Aptamers Assisted by In Silico Methods.Biomedicines · 2023Review
- Molecular Dynamics Study of the Curvature-Driven Interactions between Carbon-Based Nanoparticles and Amino Acids.Molecules (Basel, Switzerland) · 2023Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nucleic acid aptamers hold great promise for therapeutic applications due to their favorable intrinsic properties, as well as high-throughput experimental selection techniques. Despite the utility of the systematic evolution of ligands by the exponential enrichment (SELEX) method for aptamer determination, complementary in silico aptamer design is highly sought after to facilitate virtual screening and increased understanding of important nucleic acid-protein interactions. Here, with a combined experimental and theoretical approach, we have developed two optimal epithelial cellular adhesion molecule (EpCAM) aptamers. Our structure-based in silico method first predicts their binding modes and then optimizes them for EpCAM with molecular dynamics simulations, docking, and free energy calculations. Our isothermal titration calorimetry experiments further confirm that the EpCAM aptamers indeed exhibit enhanced affinity over a previously patented nanomolar aptamer, EP23. Moreover, our study suggests that EP23 and the de novo designed aptamers primarily bind to EpCAM dimers (and not monomers, as hypothesized in previous published works), suggesting a paradigm for developing EpCAM-targeted therapies.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.