Protocol for in silico characterization of natural-based molecules as quorum-sensing inhibitors
Susana Fernandes, Mariana Sousa, Fábio G. Martins, Manuel V. Simões, Sérgio Filipe Sousa · STAR Protocols · 2024
The search and development of new quorum-sensing (QS) inhibitors are ongoing processes for biofilm control. Here, we present a protocol for in silico characterization of natural-based molecules as QS inhibitors. We describe steps for preparing models of protein receptors for virtual screening. We then detail procedures for construction and virtual screening of phytochemical libraries and hit picking to be experimentally validated by in vitro assays. This protocol allows exploration of a broad range of potential inhibitors for a specific target. For complete details on the use and execution of this protocol, please refer to Fernandes et al. 1 • Instructions for identifying QS inhibitors in a large phytochemical library • Guide for preparing and performing virtual screening with multiple docking programs • Steps for computationally predicting ligand-QS receptor binding affinities Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. The search and development of new quorum-sensing (QS) inhibitors are ongoing processes for biofilm control. Here, we present a protocol for in silico characterization of natural-based molecules as QS inhibitors. We describe steps for preparing models of protein receptors for virtual screening. We then detail procedures for construction and virtual screening of phytochemical libraries and hit picking to be experimentally validated by in vitro assays. This protocol allows exploration of a broad range of potential inhibitors for a specific target.