Cleaning of Wastewater Using Crosslinked Poly(Acrylamide-co-Acrylic Acid) Hydrogels: Analysis of Rotatable Bonds, Binding Energy and Hydrogen Bonding

Hamri, Salah; Bouchaour, Tewfik; Lerari, Djahida; Bouberka, Zohra; Supiot, Philippe; Maschke, Ulrich

doi:10.3390/gels8030156

Cited by 11 publications

(9 citation statements)

References 65 publications

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“…The negative binding affinity indicates that the ligands spontaneously bind to the enzymes without consuming energy. A higher binding affinity, indicated by a more negative value, corresponds to a higher stability of the binding complex (Hamri et al., 2022). From the interaction between the substrate/reuterin and 1,3‐β‐glucan synthase, we found that UDP–glucose had a higher binding affinity than reuterin.…”

Section: Resultsmentioning

confidence: 99%

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Potential molecular mechanism of reuterin on the inhibition of Aspergillus flavus conidial germination: An in silico study

Purnawita,

Rahayu,

Lioe

et al. 2024

Journal of Food Science

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Reuterin is a natural antifungal agent derived from certain strains of Limosilactobacillus reuteri. Our previous study revealed that 6 mM reuterin inhibited completely the conidial germination of aflatoxigenic Aspergillus flavus. This study investigated the potential molecular mechanism of reuterin in inhibiting A. flavus conidial germination, which was pre‐assumed that it correlated to the inhibition of some essential enzyme activity involved in conidial germination, specifically 1,3‐β‐glucan synthase, chitin synthase, and catalases (catalase, bifunctional catalase–peroxidase, and spore‐specific catalase). The complex of 1,3‐β‐glucan synthase and chitin synthase with reuterin had a lower binding affinity than that with the substrate. Conversely, the complex of catalases with reuterin had a higher binding affinity than that with the substrate. It was suggested that 1,3‐β‐glucan synthase and chitin synthase tended to bind the substrate rather than bind reuterin. In contrast, catalases tended to bind reuterin rather than bind the substrate. Therefore, reuterin could be a potential inhibitor of catalases but may not be an inhibitor of 1,3‐β‐glucan synthase and chitin synthase. In this in silico study, we predicted that the potential molecular mechanism of reuterin in inhibiting A. flavus conidial germination was due to the inhibition of catalases activities by competitively binding to the enzymes active sites, thus resulting in the accumulation of reactive oxygen species in cells, leading to cells damage.Practical ApplicationThis in silico study revealed that reuterin is a potential inhibitor of catalases in A. flavus, thereby interfering with the antioxidant system during conidial germination. This finding shows that reuterin can be used as an antifungal agent in food or agricultural products, inhibiting conidial germination completely.

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Section: Resultsmentioning

confidence: 99%

“…A rotatable bond is defined as a single non-ring bond attached to a nonterminal non-hydrogen atom. Hamri et al (2022) reported that a higher number of rotatable bonds in the ligand allows for more conformations and improves binding activity.…”

Section: Residues In Hydrophobic Interactionmentioning

confidence: 99%

Potential molecular mechanism of reuterin on the inhibition of Aspergillus flavus conidial germination: An in silico study

Purnawita,

Rahayu,

Lioe

et al. 2024

Journal of Food Science

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“…Finally, it could have been due to the morphological changes in the cellulose materials, which influenced the dye’s accessibility within the micropore domains. In fact there is a semi-quantitative dependence between the level of the ECH content and the level of the discoloration [ 58 , 59 ].…”

Section: Resultsmentioning

confidence: 99%

An Interpenetrating Polymer Network Hydrogel Based on Cellulose, Applied to Remove Colorant Traces from the Water Medium: Electrostatic Interactions Analysis

et al. 2022

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The main objective of this work was the removal of eosin Y and green malachite from an aqueous medium by using a cellulose-based biodegradable interpenetrated network (IPN). The IPN was obtained by the sequenced synthesis method. In the first step, cellulose was crosslinked with epichlorohydrin (ECH). In the second step, the obtained gels were swollen in a reactive mixture solution, which was based on the monomers 2-hydroxyethyl methacrylate (HEMA) and 1,6- hexanediol diacrylate (HDDA). After this, swelling equilibrium was reached through the gels’ exposition to UV radiation. An infrared spectroscopy (FTIR) was used to analyze the bond stretching, which confirmed the IPN’s formation. The swelling kinetics in aqueous mediums with different pH values showed a high swelling at a basic pH value and a low response in neutral and acidic media. The IPNs showed an improvement in water uptake, compared to the networks based on PHEMA or cellulose. The IPN was used to remove dyes from the water. The results showed that a high percentage of green malachite was removed by the IPN in six minutes of contact time. The experimental results were confirmed by the docking/modeling method of the system (IPN/Dye). The different physical interactions between the IPN and the dyes’ molecules were investigated. The interactions of the hydrogen bonds with malachite green were stronger than those with eosin Y, which was in good agreement with the experimental results.

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“…A clear indication of compounds good drug absorption properties such bioavailability, intestinal absorption, Caco-2 permeability, and blood-brain barrier penetration (Francis and Chakraborty 2022;Ertl et al 2000). In addition, the number of rotatable bond were within the established limit of 6-170 rotatable bonds (Hamri et al 2022). A high number of rotatable bonds indicates high molecular flexibility, which acts as an indicator of a good oral bioavailability of the drugs (Veber et al 2002).…”

Section: Molecular Docking Evaluationmentioning

confidence: 99%

An efficient weighted network centrality approach for exploring mechanisms of action of the Ruellia herbal formula for treating rheumatoid arthritis

et al. 2023

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Aim This study outlines an efficient weighted network centrality measure approach and its application in network pharmacology for exploring mechanisms of action of the Ruellia prostrata (RP) and Ruellia bignoniiflora (RB) herbal formula for treating rheumatoid arthritis. Method In our proposed method we first calculated interconnectivity scores all the network targets then computed weighted centrality score for all targets to identify of major network targets based on centrality score. We apply our technology to network pharmacology by constructing herb-compound-putative target network; compound-putative targets-RA target network; and imbalance multi-level herb-compound-putative target-RA target-PPI network. We then identify the major targets in the network based on our centrality measure approach. Finally we validated the major identified network targets using the enrichment analysis and a molecular docking simulation. Result The results reveled our proposed weighted network centrality approach outperform classical centrality measure in identification of influential nodes in four real complex networks based on SI model simulation. Application of our approach to network pharmacology shows that 57 major targets of which 33 targets including 8 compositive compounds, 15 putative target and 10 therapeutic targets played an important role in the network and directly linked to rheumatoid arthritis. Enrichment analysis confirmed that putative targets were frequently involved in TNF, CCR5, IL-17 and G-protein coupled receptors signaling pathways which are critical in the progression of rheumatoid arthritis. The molecular docking simulation indicated four targets had significant binding affinity to major protein targets. Glyceryl diacetate-2-Oleate and Oleoyl chloride showed the best binding affinity to all targets proteins and were within Lipinski limits. ADMET prediction also confirm both compounds had no toxic effect on human hence potential lead drug compounds for treating rheumatoid arthritis. Conclusion This study developed an efficient weighted network centrality approach as tool for identification of major network targets. Network pharmacology findings provides promising results that could lead us to design and discover of alternative drug compounds. Though our approach is a purely in silico method, clinical experiments are required to test and validate the hypotheses of our computational methods.

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Cleaning of Wastewater Using Crosslinked Poly(Acrylamide-co-Acrylic Acid) Hydrogels: Analysis of Rotatable Bonds, Binding Energy and Hydrogen Bonding

Cited by 11 publications

References 65 publications

Potential molecular mechanism of reuterin on the inhibition of Aspergillus flavus conidial germination: An in silico study

Potential molecular mechanism of reuterin on the inhibition of Aspergillus flavus conidial germination: An in silico study

An Interpenetrating Polymer Network Hydrogel Based on Cellulose, Applied to Remove Colorant Traces from the Water Medium: Electrostatic Interactions Analysis

An efficient weighted network centrality approach for exploring mechanisms of action of the Ruellia herbal formula for treating rheumatoid arthritis

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