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Open AccessArticle

Adsorption of Vitamin B12 on Sugarcane-Derived Activated Carbon: Fractal Isotherm and Kinetics Modelling, Electrochemistry and Molecular Modelling Studies

by Ronald Ranguin, Mohamed Chaker Ncibi, Corine Jean-Marius, François Brouers, Gerardo Cebrián-Torrejón, Antonio Doménech-Carbó, Steffen Souila, José-Emilio Sánchez-Aparicio, Daniel Dorce, Iker Zapirain-Gysling, Jean-Didier Maréchal, Ulises Jauregui-Haza and Sarra Gaspard

Molecules 2025, 30(10), 2096; https://doi.org/10.3390/molecules30102096 - 8 May 2025

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Abstract

In the present work, the adsorption of vitamin B12 (VB12) on sugarcane-derived activated carbon (AC) was investigated with the purpose of developing a hybrid material able to degrade highly toxic and recalcitrant chlordecone (CLD) for remediating the severe environmental issue of pesticide pollution of water and soil. The AC used is made from locally accessible sugarcane bagasse. The experimental kinetic and isothermic data of VB12 adsorption on AC were modeled using multiple models, including Pseudo-Order 1 (Lagergren), Pseudo-Order 2, Elovich, and Brouers–Sotolongo models for the kinetics. The isotherms models used were Langmuir, Freundlich, Hill–Sips, Brouers–Sotolongo (BS), Brouers-Gaspard (BG), General Brouers–Sotolongo (GBS), and Redlich–Peterson (RP) models. The results showed that the BG model is the most suitable to satisfactorily describe the adsorption of VB12 on the studied AC, involving a heterogeneous adsorption mechanism onto a heterogeneous surface and providing the maximum adsorption capacity, a convenient tool to estimate the saturation level of adsorbate (i.e., chlordecone (CLD)) onto the adsorbent (AC). Voltammetric studies confirm the interaction between VB12 and the AC. Finally, molecular modeling is used to provide atomic insights showing the entrapment of VB12 inside the porous system to form a new hybrid material. The calculations provide the conformations with the best binding energy in the GaudiMM environment. Full article

(This article belongs to the Section Computational and Theoretical Chemistry)

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12 pages, 4386 KB

Open AccessArticle

Influence of Association on Binding of Disaccharides to YKL-39 and hHyal-1 Enzymes

by Agnieszka Krzemińska, José-Emilio Sánchez-Aparicio, Jean-Didier Maréchal, Agata Paneth and Piotr Paneth

Int. J. Mol. Sci. 2022, 23(14), 7705; https://doi.org/10.3390/ijms23147705 - 12 Jul 2022

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Abstract

Disaccharide complexes have been shown experimentally to be useful for drug delivery or as an antifouling surface biofilm, and are promising drug-encapsulation and delivery candidates. Although such complexes are intended for medical applications, to date no studies at the molecular level have been devoted to the influence of complexation on the enzymatic decomposition of polysaccharides. A theoretical approach to this problem has been hampered by the lack of a suitable computational tool for binding such non-covalent complexes to enzymes. Herein, we combine quantum-mechanical calculations of disaccharides complexes with a nonstandard docking GaudiMM engine that can perform such a task. Our results on four different complexes show that they are mostly stabilized by electrostatic interactions and hydrogen bonds. This strong non-covalent stabilization demonstrates the studied complexes are some excellent candidates for self-assembly smart materials, useful for drug encapsulation and delivery. Their advantage lies also in their biocompatible and biodegradable character. Full article

(This article belongs to the Special Issue State-of-the-Art Biochemistry in Poland)

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18 pages, 3954 KB

Open AccessArticle

GPathFinder: Identification of Ligand-Binding Pathways by a Multi-Objective Genetic Algorithm

by José-Emilio Sánchez-Aparicio, Giuseppe Sciortino, Daniel Viladrich Herrmannsdoerfer, Pablo Orenes Chueca, Jaime Rodríguez-Guerra Pedregal and Jean-Didier Maréchal

Int. J. Mol. Sci. 2019, 20(13), 3155; https://doi.org/10.3390/ijms20133155 - 28 Jun 2019

Cited by 16 | Viewed by 6759

Abstract

Protein–ligand docking is a widely used method to generate solutions for the binding of a small molecule with its target in a short amount of time. However, these methods provide identification of physically sound protein–ligand complexes without a complete view of the binding process dynamics, which has been recognized to be a major discriminant in binding affinity and ligand selectivity. In this paper, a novel piece of open-source software to approach this problem is presented, called GPathFinder. It is built as an extension of the modular GaudiMM platform and is able to simulate ligand diffusion pathways at atomistic level. The method has been benchmarked on a set of 20 systems whose ligand-binding routes were studied by other computational tools or suggested from experimental “snapshots”. In all of this set, GPathFinder identifies those channels that were already reported in the literature. Interestingly, the low-energy pathways in some cases indicate novel possible binding routes. To show the usefulness of GPathFinder, the analysis of three case systems is reported. We believe that GPathFinder is a software solution with a good balance between accuracy and computational cost, and represents a step forward in extending protein–ligand docking capacities, with implications in several fields such as drug or enzyme design. Full article

(This article belongs to the Special Issue New Avenues in Molecular Docking for Drug Design)

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