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Computational Identification of Potential Novel Allosteric IHF Inhibitors Using QSAR Modeling to Inhibit Plasmid-Mediated Antibiotic Resistance
(MDPI AG, 2026)
Saurith-Coronell, Oscar
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Sierra-Hernandez, Olimpo
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Rodríguez-Macías, Juan David
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Mora, José R.
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Perez-Perez, Noel
The rapid spread of antibiotic resistance through plasmid-mediated conjugation remains a primary global health concern. Despite its critical role in horizontal gene transfer, no approved drugs currently target this process, leaving a critical therapeutic gap. Integration Host Factor (IHF), a DNA-binding protein essential for plasmid replication and mobilization, emerges as a promising yet underexplored target for anti-conjugation strategies. This work aimed to develop a predictive computational model and identify small molecules that disrupt IHF function, thereby reducing plasmid transfer and limiting resistance gene dissemination. A curated dataset of 65 compounds with reported anti-plasmid activity was analyzed using a 3D-QSAR model based on algebraic descriptors computed with QuBiLS-MIDAS. The model was validated through leave-one-out cross-validation (Q2 = 0.82), Tropsha’s criteria, and Y-scrambling. Representative compounds were selected via pharmacophore clustering and evaluated through molecular docking at both the DNA-binding site and a predicted allosteric pocket of IHF. The most promising complexes underwent 200 ns molecular dynamics simulations to assess stability and interaction patterns. The QSAR model demonstrated strong predictive performance (R2 = 0.90). Docking simulations revealed more favorable binding energies at the allosteric site (up to −12.15 kcal/mol) compared to the DNA-binding site. Molecular dynamics confirmed the stability of these interactions, with allosteric complexes showing lower RMSD fluctuations and consistent binding energy profiles. Dynamic cross-correlation analysis revealed that allosteric ligand binding induces conformational changes in key catalytic residues, including Pro65, Pro61, and Leu66. These alterations may compromise DNA recognition and disrupt the initiation of replication. To our knowledge, this is the first computational study proposing allosteric inhibition of IHF as an anti-conjugation strategy. These findings provide a foundation for experimental validation and the development of novel agents to prevent horizontal gene transfer, offering a promising approach to restoring antibiotic efficacy against multidrug-resistant pathogens. ©The authors ©MDPI.
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Antimicrobial Activity of Cinnamon, Tea Tree, and Thyme Essential Oils Against Pathogenic Bacteria Isolated from Tilapia (Oreochromis spp.) in Aquaculture Farms
(MDPI, 2025)
Terrazas-Pineda, Karen A.
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Alamilla-Beltrán, Liliana
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Acero-Ortega, Claudia Ariadna
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Damas-Espinoza, Juan Antonio
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Calderón-Domínguez, Georgina
Overexploitation has led to a rise in pathogenic bacteria within aquaculture, increasing reliance on antibiotics, and developing microorganism resistance. This situation underscores the need to explore alternatives with a reduced ecological impact. Metabolites derived from essential oils have demonstrated antimicrobial properties that can inhibit or diminish the activity of various microorganisms. In this study, the antimicrobial efficacy of cinnamon (Cinnamomum zeylanicum), tea tree (Melaleuca alternifolia), and thyme (Thymus vulgaris) essential oils against pathogenic bacteria (Aeromonas, Pseudomonas, Shewanella, Comamonas, Vibrio, Acinetobacter, and Empedobacter) isolated from tilapia (Oreochromis spp.) brooded in Hidalgo State, Mexico, were investigated. Diffusion tests were conducted using discs infused with 12 different antibiotics and discs infused with essential oils at concentrations of 15, 10, and 5 μL each. Minimal inhibitory concentration tests were performed using a 96-well microplate format. All bacterial strains exhibited multi-resistance to various antibiotics; however, thyme and cinnamon effectively inhibited the tested bacteria at the lowest concentrations, while tea tree oil was the least effective. The findings suggest the potential incorporation of thyme and cinnamon as an alternative prevention to decrease the use of antibiotic treatment. ©The authors ©Molecules ©MDPI.
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Complex Networks Analyses of Antibiofilm Peptides: An Emerging Tool for Next-Generation Antimicrobials’ Discovery
(MDPI, 2023)
Agüero-Chapin, Guillermin
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Antunes, Agostinho
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Mora, José R.
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Pérez, Noel
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Contreras-Torres, Ernesto
Microbial biofilms cause several environmental and industrial issues, even affecting human health. Although they have long represented a threat due to their resistance to antibiotics, there are currently no approved antibiofilm agents for clinical treatments. The multi-functionality of antimicrobial peptides (AMPs), including their antibiofilm activity and their potential to target multiple microbes, has motivated the synthesis of AMPs and their relatives for developing antibiofilm agents for clinical purposes. Antibiofilm peptides (ABFPs) have been organized in databases that have allowed the building of prediction tools which have assisted in the discovery/design of new antibiofilm agents. However, the complex network approach has not yet been explored as an assistant tool for this aim. Herein, a kind of similarity network called the half-space proximal network (HSPN) is applied to represent/analyze the chemical space of ABFPs, aiming to identify privileged scaffolds for the development of next-generation antimicrobials that are able to target both planktonic and biofilm microbial forms. Such analyses also considered the metadata associated with the ABFPs, such as origin, other activities, targets, etc., in which the relationships were projected by multilayer networks called metadata networks (METNs). From the complex networks’ mining, a reduced but informative set of 66 ABFPs was extracted, representing the original antibiofilm space. This subset contained the most central to atypical ABFPs, some of them having the desired properties for developing next-generation antimicrobials. Therefore, this subset is advisable for assisting the search for/design of both new antibiofilms and antimicrobial agents. The provided ABFP motifs list, discovered within the HSPN communities, is also useful for the same purpose. © 2023 by the authors.
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