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Computational Approaches: Drug Discovery and Design in Medicinal Chemistry and Bioinformatics, 4th Edition

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Computational and Theoretical Chemistry".

Deadline for manuscript submissions: 16 September 2026 | Viewed by 673

Special Issue Editors


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Guest Editor
Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
Interests: oxidative stress; nutraceuticals; anticancer drugs; medicinal chemistry; drug design and discovery; molecular modeling; QSAR; pharmacophore modeling; molecular dynamics; docking; HTVS; cystic fibrosis translational readthrough inducing drugs (TRIDs)
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Palermo, Italy
Interests: medicinal chemistry; molecular modeling; QSAR; pharmacophore modeling; molecular dynamics; docking
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
Interests: synthetic medicinal chemistry; computational medicinal chemistry; anticancer compounds; translational readthrough-inducing drugs (TRIDs); nonsense mutations; natural compounds; drug repurposing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

After the great success of the first three editions, we are pleased to inform you that Molecules will launch the fourth edition of the Special Issue entitled “Computational Approaches: Drug Discovery and Design in Medicinal Chemistry and Bioinformatics, 4th Edition”.

The first three editions of the Special Issue can be found at the following links:

https://www.mdpi.com/journal/molecules/special_issues/comput_appr_drug_dis_des_med_chem_bio
https://www.mdpi.com/journal/molecules/special_issues/comput_approach_drug_II
https://www.mdpi.com/journal/molecules/special_issues/9I9ZP9D26K

In this latest Special Issue, we will continue to collect manuscripts concerning computational approaches that can improve the development of new drugs or the repurposing of an old drug for the treatment of new diseases.

In this light, structure-based approaches such as docking, induced-fit docking, molecular dynamics simulations, free energy calculations, reverse docking, and ligand-based approaches, such as molecular similarity fingerprints, shape methods, pharmacophore modeling, and QSAR, represent efficient tools to obtain insights in hit/lead identification and the optimization of small molecules and/or natural compounds. Moreover, computational approaches help to predict the metabolic fate of a drug candidate and to highlight the potential toxicity of the drug candidate, reducing the number of compounds to be tested. In the end, computational approaches were revealed to be of great interest in the field of nutraceuticals, allowing for the identification of the mechanisms of action. This Special Issue welcomes submissions from researchers in the field of drug discovery and design, including original research and review articles related to pharmaceutical sciences, pharmacology, chemical biology, and bioinformatics.

Papers combining both experimental and computational studies are encouraged.

Dr. Marco Tutone
Prof. Dr. Anna Maria Almerico
Dr. Giulia Culletta
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • QSAR and 3D-QSAR
  • unbiased and biased molecular dynamics
  • pharmacophore modeling
  • reverse modeling
  • ab initio calculations
  • protein–protein interactions
  • free energy profiling
  • modeling of nucleic acids (mRNA, rRNA, tRNA)
  • molecular docking
  • virtual screening
  • multitarget approaches
  • ADMET prediction
  • similarity analysis
  • computational approaches applied to natural compounds and nutraceuticals

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Published Papers (1 paper)

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Research

23 pages, 4916 KB  
Article
The Difluoroboranyl-Fluoroquinolone Derivative “7a” Inhibits Bacterial DNA Gyrase and Exhibits Potent Activity Against Ciprofloxacin-Resistant S. aureus In Vitro and In Vivo Using an Acute Pneumonia Model
by Luis Angel Veyna-Hurtado, Hiram Hernández-López, Denisse de Loera, Juan Manuel Vargas-Morales, Martín Muñoz-Ortega, Lorena Troncoso-Vázquez, Alondra Bocanegra-Zapata and Alberto Rafael Cervantes-Villagrana
Molecules 2026, 31(6), 1044; https://doi.org/10.3390/molecules31061044 - 20 Mar 2026
Viewed by 189
Abstract
According to the World Health Organization, antibiotic research remains insufficient, emphasizing the urgent need for new active molecules, particularly against resistant bacteria. Based on known antibacterial scaffolds, new fluoroquinolone derivatives have been synthesized by our research group, including compound 7a, a difluoroboranyl-fluoroquinolone [...] Read more.
According to the World Health Organization, antibiotic research remains insufficient, emphasizing the urgent need for new active molecules, particularly against resistant bacteria. Based on known antibacterial scaffolds, new fluoroquinolone derivatives have been synthesized by our research group, including compound 7a, a difluoroboranyl-fluoroquinolone that previously demonstrated activity against sensitive strains. Methods: The minimum inhibitory (MIC) and bactericidal (MBC) concentrations of compound 7a were determined against Staphylococcus aureus, Klebsiella pneumoniae, and Escherichia coli. The selective development of ciprofloxacin-resistant S. aureus was induced by reseeding the isolate on seven consecutive days with an antibiotic concentration that was not capable of inhibiting its development. Pharmacokinetic and toxicological properties were predicted using SwissADME, Way2Drug, and molecular docking (AutoDock Vina). In vivo toxicity was evaluated in BALB/c mice through histopathological liver and kidney analysis and serum biochemical markers. The antibacterial efficacy of 7a (80 mg/kg/day) was assessed in a murine pneumonia model induced by ciprofloxacin-resistant S. aureus. DNA gyrase inhibition was confirmed through plasmid electrophoresis assays in E. coli DH5-α cells. Results: Compound 7a exhibited both MIC and MBC values of 0.25 μg/mL, while ciprofloxacin-resistant S. aureus strains did not exhibit a detectable MIC within the concentration range tested (up to 1024 μg/mL). In silico predictions revealed favorable ADME profiles, low toxicity, and strong interaction with DNA gyrase. In vivo, 7a showed no signs of hepatotoxicity or nephrotoxicity and effectively reduced pneumonic tissue to 1.99% in infected mice. Electrophoretic assays confirmed DNA gyrase inhibition consistent with the mechanism of fluoroquinolones. Conclusions: Compound 7a evidenced activity against ciprofloxacin-resistant S. aureus in vitro and reduced infection progression in vivo. It also displays favorable drug-like properties, low predicted toxicity, and DNA gyrase inhibition. Full article
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