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Editorial Board Members’ Collection Series: QSAR and Computational Approaches to Drug Discovery

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: 20 July 2025 | Viewed by 2726

Special Issue Editors

Dr. Francisco Torrens

E-Mail Website
Guest Editor
Institut Universitari de Ciencia Molecular, Edifici d’Instituts de Paterna, P. O. Box 22085, E-46071 Valencia, Spain
Interests: theoretical chemistry; physical chemistry; mathematical chemistry; computational chemistry; molecular modelling; simulation and design; computer-aided drug design and development; molecular graphics and representation of molecular properties
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Jesús Vicente de Julián-Ortiz

E-Mail Website
Guest Editor
Department of Physical Chemistry, Faculty of Pharmacy, University of Valencia, Valencia, Spain
Interests: computational chemistry; medicinal chemistry; QSAR; QSTR
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Currently, a great effort exists to understand better and treat improvingly diseases. Computational modelling and simulation are critical in biomedical research. Computer-aided drug design and development allow understanding biomolecular interactions and the molecular mechanisms of diseases. In their applications in xenobiotics, computational methods are fundamental for drug discovery and development. This is because of their multiple uses in the collection, processing, analysis and modelling of data. In addition, they are central in associated risk assessment: Less animal testing (a currently compromised issue) is necessary. Drug design and development are multi-faceted processes in which a number of characteristics (e.g., efficacy, pharmacokinetics, safety) must be optimised. Therefore, advances in computational knowledge, artificial knowledge, machine learning and deep learning provide a basis for more effective searches of chemical spaces and the prediction of bioproperties based on molecular structure. In addition, to assess carefully the validity of the results is the most important matter. This issue aims to show different approaches and technologies that could be implemented in drug design and assessing the validity of the results, in the near future.

Dr. Francisco Torrens
Prof. Dr. Jesús Vicente de Julián-Ortiz
Guest Editors

Manuscript Submission Information

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Keywords

  • molecular modelling
  • molecular simulation
  • drug design
  • drug development
  • molecular mechanism
  • mathematical chemistry
  • structure-activity relationship
  • molecular descriptor
  • pharmacokinetics
  • toxicity

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Published Papers (2 papers)

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Research

19 pages, 5775 KiB  
Article
Effect of Lanthanide Ions and Triazole Ligands on the Molecular Properties, Spectroscopy and Pharmacological Activity
by Mauricio Alcolea Palafox, Nataliya P. Belskaya, Lozan T. Todorov, Nadya G. Hristova-Avakoumova and Irena P. Kostova
Int. J. Mol. Sci. 2024, 25(14), 7964; https://doi.org/10.3390/ijms25147964 - 21 Jul 2024
Cited by 1 | Viewed by 1024
Abstract
The effect of La, Ce, Pr and Nd ions on four Ln(ligand)3 complexes and at three DFT levels of calculation was analyzed. Four ligands were chosen, three of which were based on the 1,2,3-triazole ring. The DFT methods used were B3LYP, CAM-B3LYP [...] Read more.
The effect of La, Ce, Pr and Nd ions on four Ln(ligand)3 complexes and at three DFT levels of calculation was analyzed. Four ligands were chosen, three of which were based on the 1,2,3-triazole ring. The DFT methods used were B3LYP, CAM-B3LYP and M06-2X. The relationships established were between the geometric parameters, atomic charges, HOMO-LUMO energies and other molecular properties. These comparisons and trends will facilitate the synthesis of new complexes by selecting the ligand and lanthanide ion best suited to the desired property of the complex. The experimental IR and Raman spectra of Ln(2b′)3 complexes where Ln = La, Ce, Pr, Nd, Sm, Gd, Dy, Ho and Er ions have been recorded and compared to know the effect of the lanthanide ion on the complex. The hydration in these complexes was also analyzed. Additionally, the effect of the type of coordination center on the ability of an Ln(ligand)3 complex to participate in electron exchange and hydrogen transfer was investigated using two in vitro model systems—DPPH and ABTS. Full article
(This article belongs to the Special Issue Editorial Board Members’ Collection Series: QSAR and Computational Approaches to Drug Discovery)
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19 pages, 3186 KiB  
Article
Trimeric and Tetrameric Cationic Styryl Dyes as Novel Fluorescence and CD Probes for ds-DNA and ds-RNA
by Dijana Pavlović Saftić, Ivona Krošl Knežević, Fernando de Lera Garrido, Juan Tolosa, Dragomira Majhen, Ivo Piantanida and Joaquín Calixto García Martínez
Int. J. Mol. Sci. 2024, 25(11), 5724; https://doi.org/10.3390/ijms25115724 - 24 May 2024
Cited by 3 | Viewed by 1156
Abstract
The wide use of mono- or bis-styryl fluorophores in biomedical applications prompted the presented design and study of a series of trimeric and tetrameric homo-analogues, styryl moieties arranged around a central aromatic core. The interactions with the most common biorelevant targets, ds-DNA and [...] Read more.
The wide use of mono- or bis-styryl fluorophores in biomedical applications prompted the presented design and study of a series of trimeric and tetrameric homo-analogues, styryl moieties arranged around a central aromatic core. The interactions with the most common biorelevant targets, ds-DNA and ds-RNA, were studied by a set of spectrophotometric methods (UV-VIS, fluorescence, circular dichroism, thermal denaturation). All studied dyes showed strong light absorption in the 350–420 nm range and strongly Stokes-shifted (+100–160 nm) emission with quantum yields (Φf) up to 0.57, whereby the mentioned properties were finely tuned by the type of the terminal cationic substituent and number of styryl components (tetramers being red-shifted in respect to trimers). All studied dyes strongly interacted with ds-DNA and ds-RNA with 1–10 nM−1 affinity, with dye emission being strongly quenched. The tetrameric analogues did not show any particular selectivity between ds-DNA or ds-RNA due to large size and consequent partial, non-selective insertion into DNA/RNA grooves. However, smaller trimeric styryl series showed size-dependent selective stabilization of ds-DNA vs. ds-RNA against thermal denaturation and highly selective or even specific recognition of several particular ds-DNA or ds-RNA structures by induced circular dichroism (ICD) bands. The chiral (ICD) selectivity was controlled by the size of a terminal cationic substituent. All dyes entered efficiently live human cells with negligible cytotoxic activity. Further prospects in the transfer of ICD-based selectivity into fluorescence-chiral methods (FDCD and CPL) is proposed, along with the development of new analogues with red-shifted absorbance properties. Full article
(This article belongs to the Special Issue Editorial Board Members’ Collection Series: QSAR and Computational Approaches to Drug Discovery)
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