Molecular Modeling Applied to Nucleic Acid-Based Molecule Development

Biomolecules
Arne KrügerCarsten Wrenger

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.

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Citations

Apr 17, 2019·Nucleic Acid Therapeutics·Christopher L BarkauKeith T Gagnon
Jul 25, 2019·Nucleic Acids Research·Michiel VanmeertEveline Lescrinier
Sep 27, 2020·Journal of Molecular Modeling·Alvaro GutiérrezAlvaro Cerda
Dec 16, 2020·Proteomics·Timothy D Veenstra

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Methods Mentioned

BETA
SELEX
PCR
in silico techniques
NMR
protein folding

Software Mentioned

Dock
AMBER
Autodock Vina
ParaDock
Sym pipeline
GLAM2
Gold
DOT
RNAComposer
MEME Suite

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