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Volume 26
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Review

Role and Perspective of Molecular Simulation-Based Investigation of RNA–Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding

by
Daria V. Berdnikova
1,
Paolo Carloni
2,3,4,5,6,
Sybille Krauß
7,* and
Giulia Rossetti
2,3,6,8,*
1
Department of Chemistry–Biology, Organic Chemistry II, University of Siegen, Adolf-Reichwein-Str. 2, 57076 Siegen, Germany
2
Institute for Advanced Simulation (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany
3
Institute for Neuroscience and Medicine (INM-9), Forschungszentrum Jülich, 52425 Jülich, Germany
4
Institute of Neuroscience and Medicine (INM-11), Forschungszentrum Jülich, 52425 Jülich, Germany
5
Department of Physics, Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52056 Aachen, Germany
6
Department of Neurology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany
7
Institute of Biology (Human Biology/Neurobiology), University of Siegen, Adolf-Reichwein-Str. 2, 57076 Siegen, Germany
8
Juelich Supercomputing Center (JSC), Forschungszentrum Jülich, 52425 Jülich, Germany
*
Authors to whom correspondence should be addressed.
Molecules 2021, 26(11), 3384; https://doi.org/10.3390/molecules26113384
Submission received: 16 April 2021 / Revised: 28 May 2021 / Accepted: 1 June 2021 / Published: 3 June 2021
(This article belongs to the Special Issue RNA: Still an Under-Exploited Drug Target)
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Abstract

Aberrant RNA–protein complexes are formed in a variety of diseases. Identifying the ligands that interfere with their formation is a valuable therapeutic strategy. Molecular simulation, validated against experimental data, has recently emerged as a powerful tool to predict both the pose and energetics of such ligands. Thus, the use of molecular simulation may provide insight into aberrant molecular interactions in diseases and, from a drug design perspective, may allow for the employment of less wet lab resources than traditional in vitro compound screening approaches. With regard to basic research questions, molecular simulation can support the understanding of the exact molecular interaction and binding mode. Here, we focus on examples targeting RNA–protein complexes in neurodegenerative diseases and viral infections. These examples illustrate that the strategy is rather general and could be applied to different pharmacologically relevant approaches. We close this study by outlining one of these approaches, namely the light-controllable association of small molecules with RNA, as an emerging approach in RNA-targeting therapy.
Keywords: RNA–ligand interaction; molecular dynamics; light-controllable association RNA–ligand interaction; molecular dynamics; light-controllable association

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MDPI and ACS Style

Berdnikova, D.V.; Carloni, P.; Krauß, S.; Rossetti, G. Role and Perspective of Molecular Simulation-Based Investigation of RNA–Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding. Molecules 2021, 26, 3384. https://doi.org/10.3390/molecules26113384

AMA Style

Berdnikova DV, Carloni P, Krauß S, Rossetti G. Role and Perspective of Molecular Simulation-Based Investigation of RNA–Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding. Molecules. 2021; 26(11):3384. https://doi.org/10.3390/molecules26113384

Chicago/Turabian Style

Berdnikova, Daria V., Paolo Carloni, Sybille Krauß, and Giulia Rossetti. 2021. "Role and Perspective of Molecular Simulation-Based Investigation of RNA–Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding" Molecules 26, no. 11: 3384. https://doi.org/10.3390/molecules26113384

APA Style

Berdnikova, D. V., Carloni, P., Krauß, S., & Rossetti, G. (2021). Role and Perspective of Molecular Simulation-Based Investigation of RNA–Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding. Molecules, 26(11), 3384. https://doi.org/10.3390/molecules26113384

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