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      Antibacterial of Dibenzo- p-Dioxi-2,8-Dicarboxylic Acid Against Pathogenic Oral Bacteria E. faecalis ATCC 29212 Peptide Pheromones: Quorum Sensing of in vitro and in silico Study

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          Abstract

          Background

          Recently, it has emerged from the international scientific literature that quorum sensing (QS) is a promising way for the effective treatment of diseases caused by pathogenic bacteria. One of the crucial proteins in the QS system of Gram-positive bacteria is the pheromone. Some research has reported secondary metabolites from natural products capable of attenuating bacteria through the interruption of the quorum sensing system. One of the Indonesian herbal plants containing bioactive compounds is Sarang Semut ( Myrmecodia pendans). A phenolic compound, dibenzo- p-dioxin-2,8-dicarboxylic acid, has been isolated from this plant which had antibacterial activity against Enterococcus faecalis. However, the molecular mechanism of it has not been known.

          Aim

          The study in question aimed to predict the molecular action of the compound M. pendans against some proteins that act as a signal in the mediated QS of Gram-positive bacteria, called pheromones, including PrgQ, PrgX, PrgZ, and CcfA.

          Materials and Methods

          The methods used in this in silico study were ligand-protein docking and virtual screening that were performed by some software and programs. The compound 1 and some positive controls act as ligand were subject binding to PrgQ, PrgX, PrgZ, and CcfA as proteins target, the ligands were free for blind docking. A framework was presented potency of phenolic compounds to inhibit the protein’s target from its affinity binding scores.

          Results

          It was found thatcompound 1 was potential to inhibit all of the tested protein and gave the highest binding affinity to PrgX (−9.2 kcal.mol −1; the site at Phe59B, Phe59B, Asn63A, and Asn63B residue) and PrgZ (−7.4 kcal.mol −1; the site at Leu4B, Thr65A, Thr82A. Gln81A, and Val5B residue).

          Conclusion

          It is proposed that compound 1 has a good activity to inhibit E. faecalis through its peptide pheromones in the QS system.

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          Most cited references 35

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          Small-molecule library screening by docking with PyRx.

          Virtual molecular screening is used to dock small-molecule libraries to a macromolecule in order to find lead compounds with desired biological function. This in silico method is well known for its application in computer-aided drug design. This chapter describes how to perform small-molecule virtual screening by docking with PyRx, which is open-source software with an intuitive user interface that runs on all major operating systems (Linux, Windows, and Mac OS). Specific steps for using PyRx, as well as considerations for data preparation, docking, and data analysis, are also described.
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            Antimicrobial properties of phenolic compounds from berries.

            To investigate the antimicrobial properties of phenolic compounds present in Finnish berries against probiotic bacteria and other intestinal bacteria, including pathogenic species. Antimicrobial activity of pure phenolic compounds representing flavonoids and phenolic acids, and eight extracts from common Finnish berries, was measured against selected Gram-positive and Gram-negative bacterial species, including probiotic bacteria and the intestinal pathogen Salmonella. Antimicrobial activity was screened by an agar diffusion method and bacterial growth was measured in liquid culture as a more accurate assay. Myricetin inhibited the growth of all lactic acid bacteria derived from the human gastrointestinal tract flora but it did not affect the Salmonella strain. In general, berry extracts inhibited the growth of Gram-negative but not Gram-positive bacteria. These variations may reflect differences in cell surface structures between Gram-negative and Gram-positive bacteria. Cloudberry, raspberry and strawberry extracts were strong inhibitors of Salmonella. Sea buckthorn berry and blackcurrant showed the least activity against Gram-negative bacteria. Different bacterial species exhibit different sensitivities towards phenolics. These properties can be utilized in functional food development and in food preservative purposes.
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              Is Open Access

              CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures

               Axel Drefahl (2011)
              CurlySMILES is a chemical line notation which extends SMILES with annotations for storage, retrieval and modeling of interlinked, coordinated, assembled and adsorbed molecules in supramolecular structures and nanodevices. Annotations are enclosed in curly braces and anchored to an atomic node or at the end of the molecular graph depending on the annotation type. CurlySMILES includes predefined annotations for stereogenicity, electron delocalization charges, extra-molecular interactions and connectivity, surface attachment, solutions, and crystal structures and allows extensions for domain-specific annotations. CurlySMILES provides a shorthand format to encode molecules with repetitive substructural parts or motifs such as monomer units in macromolecules and amino acids in peptide chains. CurlySMILES further accommodates special formats for non-molecular materials that are commonly denoted by composition of atoms or substructures rather than complete atom connectivity.
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                Author and article information

                Journal
                Drug Des Devel Ther
                Drug Des Devel Ther
                DDDT
                dddt
                Drug Design, Development and Therapy
                Dove
                1177-8881
                30 July 2020
                2020
                : 14
                : 3079-3086
                Affiliations
                [1 ]Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran , Sumedang, Indonesia
                [2 ]Department of Oral Biology, Faculty of Dentistry, Universitas Padjadjaran , Sumedang, Indonesia
                Author notes
                Correspondence: Dikdik Kurnia Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran , Sumedang45363, Indonesia Tel/Fax +62-22-779-4391 Email dikdik.kurnia@unpad.ac.id
                Article
                255270
                10.2147/DDDT.S255270
                7398749
                © 2020 Kurnia et al.

                This work is published and licensed by Dove Medical Press Limited. The full terms of this license are available at https://www.dovepress.com/terms.php and incorporate the Creative Commons Attribution – Non Commercial (unported, v3.0) License ( http://creativecommons.org/licenses/by-nc/3.0/). By accessing the work you hereby accept the Terms. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed. For permission for commercial use of this work, please see paragraphs 4.2 and 5 of our Terms ( https://www.dovepress.com/terms.php).

                Page count
                Figures: 5, Tables: 3, References: 43, Pages: 8
                Categories
                Original Research

                Pharmacology & Pharmaceutical medicine

                ccfa, prgz, prgx, prgq, peptide pheromones, quorum sensing, oral bacteria

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