Protocol for in silico characterization of natural-based molecules as quorum-sensing inhibitors
Year: 2024
Type: article
Abstract: 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.
Source: STAR Protocols
Institutions: Universidade do Porto, Rede de Química e Tecnologia
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $1,500
Awards: G1240268737, G1279857300, G1509028180, ALICE - Laboratório Associado em Engenharia Química, G2863240864, G2975900969, G3029350556, Development of biocidal formulations for effective biofouling control, G3537227798, G4046065984, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, G4823118686, G5088119131, G5102272251, G545437242, G5538107981, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, G6463117426, G6701175450, G6816742654, G6997658380, G824076568, G8600706725, Laboratório Associado para a Química Verde - Tecnologias e Processos Limpos, Boosting Sustainable Innovation in Developing New Antibiotic Adjuvants to Control Biofilm Resistance
OpenAlex ID: W4403182522