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Exploring Molecular Properties Through Molecular Modeling

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: 31 March 2026 | Viewed by 207

Special Issue Editor


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Guest Editor
Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, 17071 Girona, Spain
Interests: the QSAR field of molecular property prediction; new mathematical methods; chemometric algorithms; quantitative structure-activity relationships (QSAR); quantitative structure-property relationships (QSPR); quantum chemistry;

Special Issue Information

Dear Colleagues,

One of the most promising fields in modern chemistry is molecular modeling. The concept is broad and has a significant impact on many areas, such as drug design, materials science, and biological modeling, among others. Furthermore, its applicability ranges from small-scale systems to large biological environments. In short, the main advantages of molecular modeling have been gradually proven: from the basic description of molecules, physicochemical properties can be designed, and, even more importantly, sophisticated structure–activity relationships can be predicted and interpreted. Modern and successful molecular modeling technologies exhibit the powerful ability to predict property values before chemical synthesis. This Special Issue is dedicated to presenting the state of the art in molecular modeling, showcasing both the variety of modern techniques that drive the methodology and the range of useful results that can be achieved.

Prof. Dr. Emili Besalu
Guest Editor

Manuscript Submission Information

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Keywords

  • molecular modeling
  • molecular properties
  • structure–activity relationships
  • QSAR
  • prediction
  • drug design
  • materials science
  • virtual screening
  • in-silico synthesis
  • computational chemistry
  • cheminformatics

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Published Papers (1 paper)

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Research

19 pages, 2362 KB  
Article
Enhanced Inhibition of Trametes versicolor by Structurally Modified Medicarpin: In Vitro Evaluation and In Silico Insights into Laccase Binding
by Santiago José Guevara-Martínez, José Domingo Rivera-Ramírez, Rebeca Escutia-Gutiérrez, Marco Antonio Pérez-Cisneros, Francisco Villanueva-Mejía, Stephanie García-Zavala, Rafael Herrera-Bucio and Fredy Geovannini Morales-Palacios
Int. J. Mol. Sci. 2026, 27(6), 2878; https://doi.org/10.3390/ijms27062878 (registering DOI) - 22 Mar 2026
Abstract
Medicarpin, a natural pterocarpan phytoalexin, contributes to tree defense against microbial decay, particularly from the aggressive white-rot fungus Trametes versicolor, an ASTM standard for wood durability testing. To improve upon the inhibitory effect of medicarpin against this fungus (150 mg/L), eleven derivatives were [...] Read more.
Medicarpin, a natural pterocarpan phytoalexin, contributes to tree defense against microbial decay, particularly from the aggressive white-rot fungus Trametes versicolor, an ASTM standard for wood durability testing. To improve upon the inhibitory effect of medicarpin against this fungus (150 mg/L), eleven derivatives were synthesized and evaluated. The acetylated analog demonstrated superior activity, achieving complete growth inhibition at 100 mg/L. To establish a structure–activity relationship, molecular docking was performed on the copper cluster on fungal laccase, the primary oxidative enzyme of T. versicolor. The acetylated derivative bound the T1 copper site with a more favorable free energy (−8.5 kcal/mol) than the parent compound, exhibiting enhanced stabilizing interactions and a binding pose anchored closer to the trinuclear copper cluster (TNC). These results were corroborated by 80 ns molecular dynamics simulations, confirming complex stability and the persistence of key interactions. This study demonstrates that targeted chemical modification of natural phytoalexins can significantly improve their antifungal potency. The superior performance of the acetylated medicarpin derivative, linked to optimized binding at the laccase active site, establishes a clear structure–activity relationship and highlights the potential of such engineered compounds as leads for next-generation, bio-inspired wood preservatives. Full article
(This article belongs to the Special Issue Exploring Molecular Properties Through Molecular Modeling)
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