ArticleBiophysical journal2015
Electrostatic interactions in aminoglycoside-RNA complexes.
Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 40 citations in OpenAlex.
- Shelf-stable, ready-to-use therapeutic patches: Dip-and-deliver solutions for personalized wound care.Bioengineering & translational medicine · 2026Article
- Aminoglycoside-Peptide Nucleic Acid (PNA) Conjugates against Gram-Negative Bacteria.Bioconjugate chemistry · 2025Article
- Article
- RLDOCKScore: A Scoring Function for RNA-Ligand Docking and Small Molecule Virtual Screening.Journal of chemical theory and computation · 2025Article
- 8-Oxo-7,8-dihydropurines as Building Blocks to Enhance the Selectivity of an RNA Aptamer for Aminoglycosides.ACS chemical biology · 2025Article
- Electrostatic Anchoring in RNA-Ligand Design─Dissecting the Effects of Positive Charges on Affinity, Selectivity, Binding Kinetics, and Thermodynamics.Journal of medicinal chemistry · 2025Article
- Single-Stranded Nucleic Acid Transmembrane Molecular Carriers Based on Positively Charged Helical Foldamers.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Experimental Determination of the pACS omega · 2024Article
- Conjugates of Aminoglycosides with Stapled Peptides as a Way to Target Antibiotic-Resistant Bacteria.ACS omega · 2023Article
- Systematic Review and Meta-Analysis of the Effect of Loop Diuretics on Antibiotic Pharmacokinetics.Pharmaceutics · 2023Review
- The Role of Electrostatic Interactions in IFIT5-RNA Complexes Predicted by the UBDB+EPMM Method.The journal of physical chemistry. B · 2022Article
- Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Impact of Surrounding Atoms on Electron Density from Cluster Analysis.Journal of chemical information and modeling · 2022Article
- Theoretical 3D electron diffraction electrostatic potential maps of proteins modeled with a multipolar pseudoatom data bank.Acta crystallographica. Section D, Structural biology · 2022Article
- Electron density is not spherical: the many applications of the transferable aspherical atom model.Computational and structural biotechnology journal · 2022Review
- Multinuclear Nuclear Magnetic Resonance Spectroscopy Is Used to Determine Rapidly and Accurately the Individual pACS omega · 2021Article
- Individual pACS omega · 2020Article
- Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit.Nucleic acids research · 2020Article
- Refinement of organic crystal structures with multipolar electron scattering factors.Acta crystallographica. Section A, Foundations and advances · 2020Article
- Fluorescent peptide displacement as a general assay for screening small molecule libraries against RNA.Organic & biomolecular chemistry · 2019Article
- Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides.Nucleic acids research · 2018Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Electrostatic interactions often play key roles in the recognition of small molecules by nucleic acids. An example is aminoglycoside antibiotics, which by binding to ribosomal RNA (rRNA) affect bacterial protein synthesis. These antibiotics remain one of the few valid treatments against hospital-acquired infections by Gram-negative bacteria. It is necessary to understand the amplitude of electrostatic interactions between aminoglycosides and their rRNA targets to introduce aminoglycoside modifications that would enhance their binding or to design new scaffolds. Here, we calculated the electrostatic energy of interactions and its per-ring contributions between aminoglycosides and their primary rRNA binding site. We applied either the methodology based on the exact potential multipole moment (EPMM) or classical molecular mechanics force field single-point partial charges with Coulomb formula. For EPMM, we first reconstructed the aspherical electron density of 12 aminoglycoside-RNA complexes from the atomic parameters deposited in the University at Buffalo Databank. The University at Buffalo Databank concept assumes transferability of electron density between atoms in chemically equivalent vicinities and allows reconstruction of the electron densities from experimental structural data. From the electron density, we then calculated the electrostatic energy of interaction using EPMM. Finally, we compared the two approaches. The calculated electrostatic interaction energies between various aminoglycosides and their binding sites correlate with experimentally obtained binding free energies. Based on the calculated energetic contributions of water molecules mediating the interactions between the antibiotic and rRNA, we suggest possible modifications that could enhance aminoglycoside binding affinity.
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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.