Targeting Enzymes in Drug Design and Discovery

A special issue of Pharmaceuticals (ISSN 1424-8247). This special issue belongs to the section "Biopharmaceuticals".

Deadline for manuscript submissions: 25 September 2026 | Viewed by 2070

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Special Issue Information

Dear Colleagues,

Enzymes play a central role in virtually all biological processes, acting as catalysts in metabolic pathways, signal transduction, gene expression, and many other cellular functions. Due to their specificity, catalytic efficiency, and regulatory importance, enzymes have long been recognized as prime targets in drug design and discovery. From early antibiotics and anti-inflammatory agents to modern kinase inhibitors and protease-targeted therapies, enzyme inhibition remains a cornerstone of some of the most effective therapeutic strategies across a broad spectrum of diseases.

This Special Issue aims to showcase recent advances in the identification, characterization, and therapeutic targeting of enzymes. The Issue reflects the inherently multidisciplinary nature of enzyme-centered drug discovery, incorporating insights from synthetic chemistry, structural biology, molecular modeling, pharmacology, and bioinformatics.

Topics covered in this issue include, but are not limited to, the following:

  • In silico computational modeling, including structure-based and ligand-based drug design, molecular docking, molecular dynamics simulations, bioinformatics tools, and QSAR studies;
  • Mechanistic enzymology and target validation;
  • High-throughput and virtual screening techniques;
  • Design and synthesis of small-molecule inhibitors;
  • Covalent and allosteric modulation of enzyme activity;
  • In vitro and in vivo evaluation of enzyme-targeted agents.

Particular attention will be given to enzymes implicated in cancer, neurodegeneration, infectious diseases, inflammation, and metabolic disorders, showcasing the broad therapeutic potential of enzyme modulators and reflecting the wide-ranging therapeutic potential of enzyme modulators. Submissions exploring emerging enzyme classes, novel catalytic mechanisms, and drug resistance profiles are also encouraged, as they provide critical insights into the evolving challenges of drug development.

This Special Issue welcomes high-quality original research articles, reviews, and short communications. We look forward to receiving your contributions and to advancing the field of enzyme-targeted drug discovery through this Special Issue.

Prof. Dr. Mariyana Atanasova
Guest Editor

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Keywords

  • drug design
  • computer-aided drug design (CADD)
  • molecular docking
  • molecular dynamics
  • QSAR
  • druggable proteins
  • synthesis
  • in vitro and in vivo activity evaluations
  • ADMET predictions and evaluations

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Published Papers (2 papers)

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Research

23 pages, 1864 KB  
Article
Harnessing Substituted 4-Chlorothieno[2,3-b]pyridine as a New Cap for Potent and Selective Antiproliferative HDAC Inhibitors
by Mostafa M. Badran, Berkay Beyri, Hiroshi Tateishi, Kazunori Shimagaki, Akiko Nakata, Akihiro Ito, Nao Nishimura, Samar H. Abbas, Mohamed Abdel-Aziz, Masami Otsuka, Minoru Yoshida, Mikako Fujita, Stefan Bräse and Mohamed O. Radwan
Pharmaceuticals 2026, 19(3), 442; https://doi.org/10.3390/ph19030442 - 9 Mar 2026
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Abstract
Background: Inhibition of histone deacetylase is a highly sought-after objective in the fight against cancer. Thus, the development of innovative HDAC inhibitors with significantly higher potency than SAHA against specific cancer cell types represents complex and demanding work. Method: The utilization of the [...] Read more.
Background: Inhibition of histone deacetylase is a highly sought-after objective in the fight against cancer. Thus, the development of innovative HDAC inhibitors with significantly higher potency than SAHA against specific cancer cell types represents complex and demanding work. Method: The utilization of the underexplored and privileged scaffold 4-chlorothieno[2,3-b]pyridine as a cap tethering diverse aliphatic and aromatic linkers, followed by the screening of both cellular and enzymatic activities, is undertaken in this study. Results: Compounds 7a and 9a demonstrated impressive mean GI50 values of 2.15 µM and 1.89 µM, respectively. Both compounds reduced caspase-3 levels in RPMI-8226 cells, suggesting induction of apoptosis. Compound 7a showed remarkable IC50 values of 0.37 µM, 0.58 µM, and 0.70 µM against HDACs 1, 4, and 6, respectively, consistent with the cellular assay. Additionally, compound 7a exhibited a selectivity index of 11 for RPMI-8226 cells over PBMCs, reflecting its high selectivity and potential safety. Moreover, ADMET prediction tools indicated that compounds 7a and 9b may have more favorable pharmacokinetic properties than the gold-standard HDAC inhibitor, SAHA. Conclusions: Further study and exploration of the derivatives of compounds 7a and 9a can lead to further advancement in the development of potent HDAC inhibitor anticancer drugs. Full article
(This article belongs to the Special Issue Targeting Enzymes in Drug Design and Discovery)
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27 pages, 4785 KB  
Article
Rational Design, Synthesis, and Molecular Docking of Novel Terpene Analogues of Imatinib, and Their Inhibition on Downstream BCR-ABL Signaling
by Rositsa Mihaylova, Asine Dailova-Barzeva, Irena Philipova, Georgi Momekov, Irini Doytchinova, Mariyana Atanasova and Georgi Stavrakov
Pharmaceuticals 2026, 19(2), 198; https://doi.org/10.3390/ph19020198 - 23 Jan 2026
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Abstract
Background/Objectives: Imatinib, the first tyrosine kinase inhibitor, marks the beginning of a revolution in clinical oncology. Disrupting oncogenic kinase-dependent signaling pathways represents a key strategy for advancing targeted cancer therapies. Terpene analogues of imatinib were developed to probe the influence of terminal [...] Read more.
Background/Objectives: Imatinib, the first tyrosine kinase inhibitor, marks the beginning of a revolution in clinical oncology. Disrupting oncogenic kinase-dependent signaling pathways represents a key strategy for advancing targeted cancer therapies. Terpene analogues of imatinib were developed to probe the influence of terminal ring modifications on BCR-ABL inhibition and downstream oncogenic signaling. Methods: Nine novel imatinib analogues bearing bulky aliphatic moieties were designed, synthesised, and structurally characterized by 1H/13C NMR spectroscopy and high-resolution mass spectrometry (HRMS). Molecular docking calculations were performed to assess the binding modes and intermolecular interactions. The cytotoxicity of the newly synthesized imatinib derivatives was evaluated across a panel of BCR-ABL+ leukemia cell lines. Results: Molecular docking analyses demonstrated conserved interactions within the ATP-binding site of BCR-ABL for all derivatives, with calculated docking scores ranging between 123 and 128, while modifications at the terminal ring introduced subtle changes in electrostatic and steric profiles. Biological evaluation using MTT-based cytotoxicity assays in BCR-ABL+ leukemic cell lines revealed enhanced antiproliferative activity compared with imatinib, with compounds 6a (flexible cyclohexyl) and 6d (rigid camphane-type (+)-isopinocampheyl) exhibiting the lowest micromolar activity in the AR-230 model (IC50 values of 1.1 and 1.2 μM, respectively). Proteome-wide phosphokinase profiling demonstrated shared suppression of STAT5/3/6, RSK1/2, S6K1/p70, and Pyk2, confirming effective disruption of canonical BCR-ABL pathways. Critically, the terpene moiety dictated downstream pathway bias: 6a preferentially attenuated CREB activation, whereas 6d more effectively suppressed the PI3K/Akt oncogenic axis and strongly activated proapoptotic p53-mediated stress responses. Conclusions: Our findings establish terpene-engineered imatinib analogues as tunable modulators and promising candidates for targeting downstream BCR-ABL signaling pathways in leukemia treatment. Full article
(This article belongs to the Special Issue Targeting Enzymes in Drug Design and Discovery)
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