Molecular Modeling Applied to Nucleic Acid-Based Molecule Development

Autor(es)

Kruger, Arne ^[1] ; Zimbres, Flavia M. ^{[2, 3]} ; Kronenberger, Thales ^[4] ; Wrenger, Carsten ^[1]

Afiliação do(s) autor(es)

^[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

• Tipo de documento: Artigo de Revisão
• Fonte: BIOMOLECULES; v. 8, n. 3 SEP 2018.
• Citações Web of Science: 4

Resumo

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)

• Processo FAPESP: 17/03966-4 - Alvejando a via de recuperação e biossíntese de ácido lipoico em MRSA
• Beneficiário: Carsten Wrenger
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 18/08820-0 - Inibidores da via de síntese de vitamina B6 entregues por associação com nanopartículas contra Plasmodium sp
• Beneficiário: Arne Kruger
• Modalidade de apoio: Bolsas no Brasil - Doutorado
• Processo FAPESP: 15/26722-8 - Drug discovery contra doenças infecciosas humanos
• Beneficiário: Carsten Wrenger
• Modalidade de apoio: Auxílio à Pesquisa - Temático