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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Molecular Modeling Applied to Nucleic Acid-Based Molecule Development

Full text
Author(s):
Kruger, Arne [1] ; Zimbres, Flavia M. [2, 3] ; Kronenberger, Thales [4] ; Wrenger, Carsten [1]
Total Authors: 4
Affiliation:
[1] Univ Sao Paulo, Inst Biomed Sci, Dept Parasitol, Unit Drug Discovery, BR-05508000 Sao Paulo, SP - Brazil
[2] Univ Georgia, Ctr Trop & Emerging Global Dis, Athens, GA 30602 - USA
[3] Univ Georgia, Dept Biochem & Mol Biol, Athens, GA 30602 - USA
[4] Univ Hosp Tubingen, Dept Internal Med 8, D-72076 Tubingen - Germany
Total Affiliations: 4
Document type: Review article
Source: BIOMOLECULES; v. 8, n. 3 SEP 2018.
Web of Science Citations: 4
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. (AU)

FAPESP's process: 17/03966-4 - Targeting lipoic acid salvage and biosynthesis pathways in MRSA
Grantee:Carsten Wrenger
Support Opportunities: Regular Research Grants
FAPESP's process: 18/08820-0 - Nanoparticle-assisted drug delivery of Vitamin B6 pathway inhibitors in malaria
Grantee:Arne Kruger
Support Opportunities: Scholarships in Brazil - Doctorate
FAPESP's process: 15/26722-8 - Drug discovery against human infectious diseases
Grantee:Carsten Wrenger
Support Opportunities: Research Projects - Thematic Grants