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基于计算机模拟的天然分子作为群体感应抑制剂的表征方案

Protocol for in silico characterization of natural-based molecules as quorum-sensing inhibitors.

作者信息

Fernandes Susana, Sousa Mariana, Martins Fábio G, Simões Manuel, Sousa Sérgio F

机构信息

LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.

LAQV/REQUIMTE, BioSIM, Department of Biomedicine, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal.

出版信息

STAR Protoc. 2024 Dec 20;5(4):103367. doi: 10.1016/j.xpro.2024.103367. Epub 2024 Oct 7.

DOI:10.1016/j.xpro.2024.103367
PMID:39378154
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11492069/
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..

摘要

寻找和开发新型群体感应（QS）抑制剂是控制生物膜的持续过程。在此，我们提出了一种用于基于天然的分子作为QS抑制剂的计算机模拟表征的方案。我们描述了制备用于虚拟筛选的蛋白质受体模型的步骤。然后，我们详细介绍了植物化学文库的构建和虚拟筛选以及命中物挑选的程序，这些命中物将通过体外试验进行实验验证。该方案允许探索针对特定靶点的广泛潜在抑制剂。有关该方案的使用和执行的完整详细信息，请参考费尔南德斯等人的研究。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd60/11492069/c6259ad6ad61/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd60/11492069/8e646f6388d0/fx1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd60/11492069/3c0e6d5c5116/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd60/11492069/b5975f0f56a7/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd60/11492069/4ee1fcc63ac6/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd60/11492069/c6259ad6ad61/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd60/11492069/8e646f6388d0/fx1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd60/11492069/3c0e6d5c5116/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd60/11492069/b5975f0f56a7/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd60/11492069/4ee1fcc63ac6/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd60/11492069/c6259ad6ad61/gr4.jpg

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The action of phytochemicals in biofilm control.植物化学物质在生物膜控制中的作用。
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Liposomal Formulations Loaded with a Eugenol Derivative for Application as Insecticides: Encapsulation Studies and In Silico Identification of Protein Targets.
负载丁香酚衍生物的脂质体制剂用作杀虫剂：包封研究及蛋白质靶点的计算机模拟鉴定
Nanomaterials (Basel). 2022 Oct 13;12(20):3583. doi: 10.3390/nano12203583.
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Selection of Bis-Indolyl Pyridines and Triphenylamines as New Inhibitors of SARS-CoV-2 Cellular Entry by Modulating the Spike Protein/ACE2 Interfaces.选择双吲哚基吡啶和三苯胺作为新型 SARS-CoV-2 细胞进入抑制剂，通过调节刺突蛋白/ACE2 界面。
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Screening strategies for quorum sensing inhibitors in combating bacterial infections.用于对抗细菌感染的群体感应抑制剂的筛选策略。
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New carvacrol and thymol derivatives as potential insecticides: synthesis, biological activity, computational studies and nanoencapsulation.新型香芹酚和百里香酚衍生物作为潜在杀虫剂：合成、生物活性、计算研究及纳米包封
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