ArticleFrontiers in chemistry2020
Exploring the RNA-Recognition Mechanism Using Supervised Molecular Dynamics (SuMD) Simulations: Toward a Rational Design for Ribonucleic-Targeting Molecules?
Article in Frontiers in chemistry, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Capturing Hu Antigen R Domain Closure Through Supervised Molecular Dynamics Simulations.ChemMedChem · 2026Article
- In silico designing of small molecules for targeting RNA: current landscape and future directions.Journal of computer-aided molecular design · 2026Review
- Structuring Disorder via Supervised Molecular Dynamics: Uncovering Arginine-Glycine-Glycine-Mediated Ribonucleic Acid-Intrinsically Disordered Region Recognition Mechanisms.Journal of chemical information and modeling · 2026Article
- Molecular dynamics simulations of proteins: an in-depth review of computational strategies, structural insights, and their role in medicinal chemistry and drug development.Biological cybernetics · 2025Review
- Fighting Antimicrobial Resistance: Insights on How theJournal of chemical information and modeling · 2023Article
- Dynamic docking of small molecules targeting RNA CUG repeats causing myotonic dystrophy type 1.Biophysical journal · 2023Article
- RNA-protein complexes and force field polarizability.Frontiers in chemistry · 2023Article
- Thermal titration molecular dynamics (TTMD): shedding light on the stability of RNA-small molecule complexes.Frontiers in molecular biosciences · 2023Article
- Investigating RNA-protein recognition mechanisms through supervised molecular dynamics (SuMD) simulations.NAR genomics and bioinformatics · 2022Article
- Geneticin shows selective antiviral activity against SARS-CoV-2 by interfering with programmed -1 ribosomal frameshifting.Antiviral research · 2022Article
- Protein DEK and DTA Aptamers: Insight Into the Interaction Mechanisms and the Computational Aptamer Design.Frontiers in molecular biosciences · 2022Article
- Shedding Light on the Molecular Recognition of Sub-Kilodalton Macrocyclic Peptides on Thrombin by Supervised Molecular Dynamics.Frontiers in molecular biosciences · 2021Article
- Exploring Ligand Binding to Calcitonin Gene-Related Peptide Receptors.Frontiers in molecular biosciences · 2021Article
- RNA-ligand molecular docking: advances and challenges.Wiley interdisciplinary reviews. Computational molecular scienceArticle
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although proteins have represented the molecular target of choice in the development of new drug candidates, the pharmaceutical importance of ribonucleic acids has gradually been growing. The increasing availability of structural information has brought to light the existence of peculiar three-dimensional RNA arrangements, which can, contrary to initial expectations, be recognized and selectively modulated through small chemical entities or peptides. The application of classical computational methodologies, such as molecular docking, for the rational development of RNA-binding candidates is, however, complicated by the peculiarities characterizing these macromolecules, such as the marked conformational flexibility, the singular charges distribution, and the relevant role of solvent molecules. In this work, we have thus validated and extended the applicability domain of SuMD, an all-atoms molecular dynamics protocol that allows to accelerate the sampling of molecular recognition events on a nanosecond timescale, to ribonucleotide targets of pharmaceutical interest. In particular, we have proven the methodological ability by reproducing the binding mode of viral or prokaryotic ribonucleic complexes, as well as that of artificially engineered aptamers, with an impressive degree of accuracy.
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