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Application and evaluation of molecular docking for aptamer and small molecular interaction - A case study with tetracycline antibiotics by Gang Liang; Jie Zhao; Yufei Gao; Tao Xie; Jianhui Zhen; Ligang Pan; Wenwen Gong is a Chemistry article available to read on EtoBox.

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Molecular docking (MD) analysis is currently the most commonly used theoretical simulation method to investigate the interaction of aptamers (receptors) and small molecules (ligands) and understand the recognition mechanism between them at a molecular level. Using the specific aptamers of tetracycline antibiotics (tetracycline (TET), oxytetracycline (OTC), doxycycline (DOC)) as the docking models, three steady-state aptamers of tertiary structures (SATS) were established for each aptamer with the UNAFold and RNAComposer tools. The binding free energy (BFE), docking score (DS), and binding site (base) of the specific ligands (TET, OTC, and DOC) with their respective SATS were obtained by molecular docking. The results revealed one or more binding sites in the established SATS of the aptamers. The BFE and DS of different binding sites of one specific SATS varied significantly. The results also revealed that the site with the highest BFE represented the most dominant binding site, even if it was not the SATS with minimum energy. The BFE values could also be used to evaluate the affinity and specificity of the aptamer to its target. For the first time, this study proposes a method for

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Author

Gang Liang; Jie Zhao; Yufei Gao; Tao Xie; Jianhui Zhen; Ligang Pan; Wenwen Gong

Publisher

Elsevier BV

Published

2024

Language

EN

Field

Chemistry (Physical Sciences)