Advances in Rational Drug Design: From Target Identification to Drug Lead Compounds

A special issue of Chemistry (ISSN 2624-8549). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: 20 January 2026 | Viewed by 3860

Special Issue Editors


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Guest Editor
Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
Interests: drug discovery; molecular modeling; nutraceutical modeling; bioinformatics; medicinal chemistry
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Department of Pharmacy, “Drug Discovery Lab”, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
Interests: drug discovery; medicinal chemistry; molecular modeling; polypharmacology; artificial intelligence; machine learning
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The landscape of drug discovery is rapidly evolving through the integration of innovative computational and experimental approaches. Rational drug design, encompassing both structure-based and ligand-based strategies, has accelerated the identification of novel drug leads by leveraging insights into molecular targets, bioinformatics, and cheminformatics. Advances in artificial intelligence, machine learning, molecular dynamics, and virtual screening are reshaping how researchers predict drug–target interactions, optimize lead compounds, and evaluate pharmacokinetic properties. This Special Issue invites original research articles, reviews, and perspectives on recent developments in target identification, hit-to-lead optimization, computer-aided drug design (CADD), deep learning applications in medicinal chemistry, and the modeling of small molecules and biologics. Contributions exploring multidisciplinary approaches, including the use of big data, multi-omics integration, and innovative experimental validation techniques, are particularly encouraged. We aim to gather a diverse collection of studies to reflect the dynamic cross-disciplinary nature of modern drug discovery and foster knowledge exchange across computational and experimental domains.

Topics of interest include but are not limited to:

  • computer-aided drug discovery (CADD);
  • rational drug design;
  • target identification;
  • lead optimization;
  • molecular modeling;
  • virtual screening;
  • deep learning in drug discovery;
  • ADMET prediction;
  • bioinformatics;
  • artificial intelligence in medicinal chemistry.

We invite you to submit your work to this Special Issue. Full papers, communications, and reviews are all welcome.

Dr. Carmen Di Giovanni
Prof. Dr. Antonio Lavecchia
Guest Editors

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Keywords

  • computer aided-drug discovery
  • drug development
  • lead compounds
  • drug candidates
  • molecular modeling
  • structure-based drug design
  • ligand-based drug design
  • artificial intelligence (AI)

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Published Papers (3 papers)

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Research

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24 pages, 2449 KB  
Article
Synthesis and Characterization of a New Hydrogen-Bond-Stabilized 1,10-Phenanthroline–Phenol Schiff Base: Integrated Spectroscopic, Electrochemical, Theoretical Studies, and Antimicrobial Evaluation
by Alexander Carreño, Evys Ancede-Gallardo, Ana G. Suárez, Marjorie Cepeda-Plaza, Mario Duque-Noreña, Roxana Arce, Manuel Gacitúa, Roberto Lavín, Osvaldo Inostroza, Fernando Gil, Ignacio Fuentes and Juan A. Fuentes
Chemistry 2025, 7(4), 135; https://doi.org/10.3390/chemistry7040135 - 21 Aug 2025
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Abstract
A new Schiff base, (E)-2-(((1,10-phenanthrolin-5-yl)imino)methyl)-4,6-di-tert-butylphenol (Fen-IHB), was designed to incorporate an intramolecular hydrogen bond (IHB) between the phenolic OH and the azomethine nitrogen with the goal of modulating its physicochemical and biological properties. Fen-IHB was synthesized by condensation of [...] Read more.
A new Schiff base, (E)-2-(((1,10-phenanthrolin-5-yl)imino)methyl)-4,6-di-tert-butylphenol (Fen-IHB), was designed to incorporate an intramolecular hydrogen bond (IHB) between the phenolic OH and the azomethine nitrogen with the goal of modulating its physicochemical and biological properties. Fen-IHB was synthesized by condensation of 5-amino-1,10-phenanthroline with 3,5-di-tert-butyl-2-hydroxybenzaldehyde and exhaustively characterized by HR-ESI-MS, FTIR, 1D/2D NMR (1H, 13C, DEPT-45, HH-COSY, CH-COSY, D2O exchange), and UV–Vis spectroscopy. Cyclic voltammetry in anhydrous CH3CN revealed a single irreversible cathodic peak at −1.43 V (vs. Ag/Ag+), which is consistent with the intramolecular reductive coupling of the azomethine moiety. Density functional theory (DFT) calculations, including MEP mapping, Fukui functions, dual descriptor analysis, and Fukui potentials with dual descriptor potential, identified the exocyclic azomethine carbon as the principal nucleophilic site and the phenolic ring (hydroxyl oxygen and adjacent carbons) as the main electrophilic region. Noncovalent interaction (NCI) analysis further confirmed the strength and geometry of the intramolecular hydrogen bond (IHB). In vitro antimicrobial assays indicated that Fen-IHB was inactive against Gram-negative facultative anaerobes (Salmonella enterica serovar Typhimurium and Typhi, Escherichia coli) and strictly anaerobic Gram-positive species (Clostridioides difficile, Roseburia inulinivorans, Blautia coccoides), as any growth inhibition was indistinguishable from the DMSO control. Conversely, Fen-IHB displayed measurable activity against Gram-positive aerobes and aerotolerant anaerobes, including Bacillus subtilis, Streptococcus pyogenes, Enterococcus faecalis, Staphylococcus aureus, and Staphylococcus haemolyticus. Overall, these comprehensive characterization results confirm the distinctive chemical and electronic properties of Fen-IHB, underlining the crucial role of the intramolecular hydrogen bond and electronic descriptors in defining its reactivity profile and selective biological activity. Full article
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21 pages, 3617 KB  
Article
Characterization and Computational Insights into the Potential Biological Activity of 4-Hydroxyphenyl 8-Chlorooctanoate Purified from Endophytic Fusarium solani
by Muhammad Salim, Sajjad Ahmad and Saeed Ullah Khattak
Chemistry 2025, 7(4), 130; https://doi.org/10.3390/chemistry7040130 - 14 Aug 2025
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Abstract
Endophytes are important sources of bioactive secondary metabolites with therapeutic and agricultural relevance. This study reports the isolation and characterization of bioactive compounds from endophytic Fusarium solani associated with Solanum surattense. The fungal strain, selected after preliminary screening for its antimicrobial potential, [...] Read more.
Endophytes are important sources of bioactive secondary metabolites with therapeutic and agricultural relevance. This study reports the isolation and characterization of bioactive compounds from endophytic Fusarium solani associated with Solanum surattense. The fungal strain, selected after preliminary screening for its antimicrobial potential, was identified through morphological and molecular methods. A pure compound, 4-hydroxyphenyl 8-chlorooctanoate with a molecular mass of 270, was obtained and structurally characterized using GC–MS, FTIR, and NMR spectroscopy. Its anti-microbial potential was evaluated through molecular docking against key bacterial (Staphylococcus aureus) and fungal (Aspergillus fumigatus) targets, showing notable binding affinities with ClpP protease (−7.1 kcal/mol) and 14α-demethylase (−7.4 kcal/mol), respectively. Molecular dynamics simulations further confirmed the stability of the 5FRB-compound complex, with lower RMSD and RMSF values indicating strong structural integrity. Supporting analyses (B-factor and radius of gyration) confirmed the compactness and rigidity of the complex. These findings highlight the potential of 4-hydroxyphenyl 8-chlorooctanoate as a promising antimicrobial agent and provide a strong basis for further in vitro and in vivo validation of the purified compound as an antimicrobial candidate. Full article
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Review

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38 pages, 2987 KB  
Review
Benzothiazole-Based Therapeutics: FDA Insights and Clinical Advances
by Subba Rao Cheekatla
Chemistry 2025, 7(4), 118; https://doi.org/10.3390/chemistry7040118 - 25 Jul 2025
Viewed by 1526
Abstract
Benzothiazole derivatives have emerged as being highly significant in drug discovery due to their versatile biological activities and structural adaptability. Incorporating nitrogen and sulfur, this fused heterocyclic scaffold exhibits wide-ranging pharmacological properties, including anticancer, antimicrobial, anti-inflammatory, antidiabetic, neuroprotective, and diagnostic applications. A diverse [...] Read more.
Benzothiazole derivatives have emerged as being highly significant in drug discovery due to their versatile biological activities and structural adaptability. Incorporating nitrogen and sulfur, this fused heterocyclic scaffold exhibits wide-ranging pharmacological properties, including anticancer, antimicrobial, anti-inflammatory, antidiabetic, neuroprotective, and diagnostic applications. A diverse set of clinically approved and investigational compounds, such as flutemetamol for Alzheimer’s diagnosis, riluzole for ALS, and quizartinib for AML, illustrates the scaffold’s therapeutic potential in varied applications. These agents act via mechanisms such as enzyme inhibition, receptor modulation, and amyloid imaging, demonstrating the scaffold’s high binding affinity and target specificity. Advances in synthetic strategies and our understanding of structure–activity relationships (SARs) continue to drive the development of novel benzothiazole-based therapeutics with improved potency, selectivity, and safety profiles. We also emphasize recent in vitro and in vivo studies, including drug candidates in clinical trials, to provide a comprehensive perspective on the therapeutic potential of benzothiazole-based compounds in modern drug discovery. This review brings together recent progress to help guide the development of new benzothiazole-based compounds for future therapeutic applications. Full article
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