The Biofilms Structural Database

Magalhães, Rita P.; Vieira, Tatiana F.; Fernandes, Henrique S.; Melo, André; Simões, Manuel; Sousa, Sérgio F.

doi:10.1016/j.tibtech.2020.04.002

Cited by 19 publications

(22 citation statements)

References 15 publications

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“…The structures were identified using the Biofilms Structural Database [ 38 ] and then downloaded from the Protein Data Bank [ 39 ]. These X-ray structures and the corresponding resolution value, ligand and bacterial strain are summarized in Table 1 .…”

Section: Methodsmentioning

confidence: 99%

Identification of New Potential Inhibitors of Quorum Sensing through a Specialized Multi-Level Computational Approach

2021

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Biofilms are aggregates of microorganisms anchored to a surface and embedded in a self-produced matrix of extracellular polymeric substances and have been associated with 80% of all bacterial infections in humans. Because bacteria in biofilms are less amenable to antibiotic treatment, biofilms have been associated with developing antibiotic resistance, a problem that urges developing new therapeutic options and approaches. Interfering with quorum-sensing (QS), an important process of cell-to-cell communication by bacteria in biofilms is a promising strategy to inhibit biofilm formation and development. Here we describe and apply an in silico computational protocol for identifying novel potential inhibitors of quorum-sensing, using CviR—the quorum-sensing receptor from Chromobacterium violaceum—as a model target. This in silico approach combines protein-ligand docking (with 7 different docking programs/scoring functions), receptor-based virtual screening, molecular dynamic simulations, and free energy calculations. Particular emphasis was dedicated to optimizing the discrimination ability between active/inactive molecules in virtual screening tests using a target-specific training set. Overall, the optimized protocol was used to evaluate 66,461 molecules, including those on the ZINC/FDA-Approved database and to the Mu.Ta.Lig Virtual Chemotheca. Multiple promising compounds were identified, yielding good prospects for future experimental validation and for drug repurposing towards QS inhibition.

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Section: Methodsmentioning

confidence: 99%

Identification of New Potential Inhibitors of Quorum Sensing through a Specialized Multi-Level Computational Approach

2021

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“…Stainless steel is one of the most employed materials in the construction of food equipment, mainly because of its high durability and resistance to corrosion [17]. However, most of the pathogens involved in food-borne diseases can adhere to the majority of materials encountered in food production plants, and several reports have demonstrated the ability of bacterial cells to produce biofilms on the aforementioned materials [5,22,23].…”

Section: Formation Of Microbial Biofilms On Surfaces In the Food Industrymentioning

confidence: 99%

“…The qPCR method can evaluate specific gene expression along with the quantification of bacterial populations in dual-species biofilms when the profusion of gene transcription is calculated by normalization against ref mRNA [41]. The sensitivity of qPCR to quantify species with extremely low cell numbers may limit its ability to quantify less prevalent species in the community [5,41].…”

Section: Detection Of Biofilms On Surfaces In the Food Industrymentioning

confidence: 99%

“…Ideally, preventing biofilm formation seems more logical than removing it [5]. Therefore, the prevention of foodborne diseases that can be transmitted by surface contamination of equipment and utensils is based on the efficient reduction of pathogens by proper washing and disinfection by biocides [42,43].…”

Section: Surface Cleaning and Disinfection Strategies For Prevention Of Microbial Biofilmsmentioning

confidence: 99%

“…In food processing environments, biofilms are the major cause for the persistence of bacterial cells on food contact surfaces such as equipment and utensils, hence constituting a continuous source of food contamination [3,4]. Thus, most of the pathogenic or spoilage bacteria in food production systems can be detected on surfaces in the form of planktonic or attached cells, or in community arrangements as a biofilm [5]. For example, there is evidence on the ability of Staphylococcus aureus and Listeria monocytogenes to adhere on the surfaces of food contact materials including stainless steel, rubber, polypropylene, and glass, as well as on the surface of food products [6].…”

Section: Introductionmentioning

confidence: 99%

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Biofilms from Pathogenic Bacteria in Food Processing Environments: Formation and Preventive Disinfection Procedures

Lee

Portinari

Corassin

et al. 2021

Food Science and Engineering

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The ability of some pathogenic bacterial species to form biofilms on surfaces of equipment and utensils is of great concern to the food industry since they represent a continuous source of contamination in food processing environments. In this review, the factors involved in the formation of microbial biofilms are highlighted, along with a discussion on the preventive disinfection procedures recommended to avoid the attachment of microbial cells on surfaces of equipment and utensils in food processing areas. Relevant articles published in the last 10 years (2012-present) were selected in PubMed, Science Direct, and Google Scholar. Methods for assessing the adhesion and biofilm formation ability of strains isolated from surfaces in the food industry environment are also presented.

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Spatiotemporal Release of Reactive Oxygen Species and NO for Overcoming Biofilm Heterogeneity

et al. 2022

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The heterogeneity in biofilms is a major challenge in biofilm therapies due to different susceptibility of bacteria and extracellular polymeric substances (EPS) to antibacterial agents. Here, we describe a therapeutic strategy that overcame biofilm heterogeneity, where antibacterial agent (NO) and EPS dispersant (reactive oxygen species (ROS)‐inducing Fe3+) were separately loaded in the yolk and shell compartment of a yolk–shell nanoplatform. Compared with traditional combinational chemotherapies which suffer from inconsistent pharmacokinetics profiles, this strategy drew on the pharmacokinetic complementarity of ROS and NO, where ROS with a short diffusion distance and a high redox potential corrupted the EPS, facilitating NO, which has a long diffusion distance and a broad antimicrobial spectrum, to penetrate the biofilm and eliminate the resident bacteria. Additionally, the construction of a three‐dimensional spherical biofilm model is novel and clinically relevant.

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The Biofilms Structural Database

Cited by 19 publications

References 15 publications

Identification of New Potential Inhibitors of Quorum Sensing through a Specialized Multi-Level Computational Approach

Identification of New Potential Inhibitors of Quorum Sensing through a Specialized Multi-Level Computational Approach

Biofilms from Pathogenic Bacteria in Food Processing Environments: Formation and Preventive Disinfection Procedures

Spatiotemporal Release of Reactive Oxygen Species and NO for Overcoming Biofilm Heterogeneity

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