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Biomolecules 2018, 8(3), 83; https://doi.org/10.3390/biom8030083

Molecular Modeling Applied to Nucleic Acid-Based Molecule Development

1
Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
2
Department of Biochemistry and Molecular Biology and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
3
Department of Internal Medicine VIII, University Hospital of Tübingen, 72076 Tübingen, Germany
*
Author to whom correspondence should be addressed.
Received: 31 July 2018 / Revised: 12 August 2018 / Accepted: 16 August 2018 / Published: 27 August 2018
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Abstract

Molecular modeling by means of docking and molecular dynamics (MD) has become an integral part of early drug discovery projects, enabling the screening and enrichment of large libraries of small molecules. In the past decades, special emphasis was drawn to nucleic acid (NA)-based molecules in the fields of therapy, diagnosis, and drug delivery. Research has increased dramatically with the advent of the SELEX (systematic evolution of ligands by exponential enrichment) technique, which results in single-stranded DNA or RNA sequences that bind with high affinity and specificity to their targets. Herein, we discuss the role and contribution of docking and MD to the development and optimization of new nucleic acid-based molecules. This review focuses on the different approaches currently available for molecular modeling applied to NA interaction with proteins. We discuss topics ranging from structure prediction to docking and MD, highlighting their main advantages and limitations and the influence of flexibility on their calculations. View Full-Text
Keywords: aptamers; docking; molecular dynamics; nucleic acids aptamers; docking; molecular dynamics; nucleic acids
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).
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Krüger, A.; Zimbres, F.M.; Kronenberger, T.; Wrenger, C. Molecular Modeling Applied to Nucleic Acid-Based Molecule Development. Biomolecules 2018, 8, 83.

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