Computational screening of natural compounds as putative quorum sensing inhibitors targeting drug resistance bacteria: Molecular docking and molecular dynamics simulations

Chaieb, Kamel; Kouidhi, Bochra; Hosawi, Salman; Baothman, Othman A.; Zamzami, Mazin A.; Altayeb, Hisham N.

doi:10.1016/j.compbiomed.2022.105517

Cited by 45 publications

(21 citation statements)

References 65 publications

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“…In addition, the binding interaction between the FGMA/FG/PA hydrogel and S. aureus fibronectin‐binding proteins (FnBPs) was analyzed by molecular docking. [ 29 ] Consequently, PA forms three hydrogen bonds with FnBPs, as shown in Figure 3I, and the three hydrogen bonds are GLY‐304 (2.5 Å), ASN‐303 (3.2 Å), and ILE‐159 (3.2 Å). Since FnBPs are targets for bacterial binding to host cells, they affect bacterial adhesion and invasion of host cells.…”

Section: Resultsmentioning

confidence: 99%

All‐Natural Immunomodulatory Bioadhesive Hydrogel Promotes Angiogenesis and Diabetic Wound Healing by Regulating Macrophage Heterogeneity

et al. 2023

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Macrophages are highly heterogeneous and exhibit a diversity of functions and phenotypes. They can be divided into pro‐inflammatory macrophages (M1) and anti‐inflammatory macrophages (M2). Diabetic wounds are characterized by a prolonged inflammatory phase and difficulty in healing due to the accumulation of pro‐inflammatory (M1) macrophages in the wound. Therefore, hydrogel dressings with macrophage heterogeneity regulation function hold great promise in promoting diabetic wound healing in clinical applications. However, the precise conversion of pro‐inflammatory M1 to anti‐inflammatory M2 macrophages by simple and biosafe approaches is still a great challenge. Here, an all‐natural hydrogel with the ability to regulate macrophage heterogeneity is developed to promote angiogenesis and diabetic wound healing. The protocatechuic aldehyde hybridized collagen‐based all‐natural hydrogel exhibits good bioadhesive and antibacterial properties as well as reactive oxygen species scavenging ability. More importantly, the hydrogel is able to convert M1 macrophages into M2 macrophages without the need for any additional ingredients or external intervention. This simple and safe immunomodulatory approach shows great application potential for shortening the inflammatory phase of diabetic wound repair and accelerating wound healing.

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Section: Resultsmentioning

confidence: 99%

All‐Natural Immunomodulatory Bioadhesive Hydrogel Promotes Angiogenesis and Diabetic Wound Healing by Regulating Macrophage Heterogeneity

et al. 2023

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“…The radius of gyration (ROG) is used to calculate the spread of mass of ligands around their geometrical central axis [ 35 ], whereas firmer structures are associated with low ROG values, while high value indicates a more labile character of the complex [ 36 ]. Nadide, denufosol and cangrelor-Mpro complexes displayed a rGyr varied between 4.3–7, 4.5–7, 4.8–6.9 and 4.8–6.9Ả, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…With respect to the molecular surface (MolSA), which corresponds to the Van der Waals surface, nadide and cangrelor showed more constant fluctuations in MolsA values compared to denufosol. While solvent accessible surface area (SASA) shows the solvent-like behaviour of the protein–ligand complex, a lower value indicates the stability of the system [ 36 ]. Results obtained showed that the lowest SASA value was observed with nadide.…”

Section: Resultsmentioning

confidence: 99%

Drug repurposing against main protease and RNA-dependent RNA polymerase of SARS-CoV-2 using molecular docking, MM-GBSA calculations and molecular dynamics

et al. 2022

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A virus called severe acute respiratory distress syndrome coronavirus type 2 (SARS‐CoV‐2) is the causing organism of coronavirus disease 2019 (COVID-19), which has severely affected human life and threatened public health. The pandemic took millions of lives worldwide and caused serious negative effects on human society and the economy. SARS-CoV-2 main protease (Mpro) and RNA-dependent RNA polymerase (RdRp) are interesting targets due to their crucial role in viral replication and growth. Since there is only one approved therapy for COVID-19, drug repurposing is a promising approach to finding molecules with potential activity against COVID-19 in a short time and at minimal cost. In this study, virtual screening was performed on the ChEMBL library containing 9923 FDA-approved drugs, using various docking filters with different accuracy. The best drugs with the highest docking scores were further examined for molecular dynamics (MD) studies and MM-GBSA calculations. The results of this study suggest that nadide, cangrelor and denufosol are promising potential candidates against COVID-19. Further in vitro, preclinical and clinical studies of these candidates would help to discover safe and effective anti-COVID-19 drugs.

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“…The regulatory mechanism of the bacterial QS system has been extensively studied. It has been found that the system can be targeted for the development of antibacterial inhibitors, and such inhibitors are called Quorum Sensing Inhibitors (QSIs; Chaieb et al, 2022 ). In addition to common antimicrobial peptides and antibiotics, many natural active substances extracted from TCMs and plants are also QSIs that can play an important role in the regulation of bacterial biofilm formation.…”

Section: Quorum Sensingmentioning

confidence: 99%

Recent advances on the regulation of bacterial biofilm formation by herbal medicines

Zhang

Wang

et al. 2022

Front. Microbiol.

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Biofilm formation is a fundamental part of life cycles of bacteria which affects various aspects of bacterial-host interactions including the development of drug resistance and chronic infections. In clinical settings, biofilm-related infections are becoming increasingly difficult to treat due to tolerance to antibiotics. Bacterial biofilm formation is regulated by different external and internal factors, among which quorum sensing (QS) signals and nucleotide-based second messengers play important roles. In recent years, different kinds of anti-biofilm agents have been discovered, among which are the Chinese herbal medicines (CHMs). CHMs or traditional Chinese medicines have long been utilized to combat various diseases around the world and many of them have the ability to inhibit, impair or decrease bacterial biofilm formation either through regulation of bacterial QS system or nucleotide-based second messengers. In this review, we describe the research progresses of different chemical classes of CHMs on the regulation of bacterial biofilm formation. Though the molecular mechanisms on the regulation of bacterial biofilm formation by CHMs have not been fully understood and there are still a lot of work that need to be performed, these studies contribute to the development of effective biofilm inhibitors and will provide a novel treatment strategy to control biofilm-related infections.

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Computational screening of natural compounds as putative quorum sensing inhibitors targeting drug resistance bacteria: Molecular docking and molecular dynamics simulations

Cited by 45 publications

References 65 publications

All‐Natural Immunomodulatory Bioadhesive Hydrogel Promotes Angiogenesis and Diabetic Wound Healing by Regulating Macrophage Heterogeneity

All‐Natural Immunomodulatory Bioadhesive Hydrogel Promotes Angiogenesis and Diabetic Wound Healing by Regulating Macrophage Heterogeneity

Drug repurposing against main protease and RNA-dependent RNA polymerase of SARS-CoV-2 using molecular docking, MM-GBSA calculations and molecular dynamics

Recent advances on the regulation of bacterial biofilm formation by herbal medicines

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