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Enzyme Inhibitors: Design, Synthesis and Biological Evaluation—3rd Edition

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: 31 May 2026 | Viewed by 3381

Special Issue Editors


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Guest Editor
Department of Neurofarba, Pharmaceutical and Nutraceutical Section, University of Florence, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
Interests: medicinal chemistry; drug design; organic synthesis; enzyme inhibition; channel blockers; G protein-coupled receptors (GPCRs); ligands
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Guest Editor
Department of Chemistry, Northern Michigan University, 1401 Presque Isle Avenue, Marquette, MI 49855, USA
Interests: medicinal plants; drug discovery from plants; enzymology; alkaloids; mass spectrometry; metabolomics; ethnopharmacology; enzyme inhibitors
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Enzymes are specialized proteins that increase the speed of chemical reactions, thus acting as biocatalysts. In the human body, enzymes catalyze all kinds of chemical reactions, playing vital roles in digestion and metabolism, blood coagulation, neuronal signaling, DNA repair, and replication, as well as many other functions. Under physiological conditions, an enzyme works by first binding to its substrate, forming an enzyme–substrate complex, which is then converted into the final product. The final product then dissociates from the enzyme, and a new catalytic cycle begins. Although they are crucial in maintaining life, dysfunctional, improperly regulated, over-active, or over-expressed enzymes contribute to the pathology of many diseases. Both naturally derived and synthetic molecules can bind to enzymes and alter their catalytic activity, and, in most cases, reduce enzyme activity. Many of these enzyme inhibitors are approved drugs, and enzyme inhibition continues to play a pivotal role in medicinal chemistry. A primary understanding of the action of enzyme inhibitors is fundamental in the development of new therapeutic agents. This Special Issue will focus on all aspects of enzyme inhibitors, ranging from the design and synthesis of these compounds to their pharmacological evaluation and computational modeling and structural biology studies designed to elucidate the interactions between inhibitors and enzymes. Papers that focus on innovative aspects or novel mechanisms in enzyme inhibition are also welcome. We hope that this Special Issue stimulates authors and readers and makes an important contribution to the field of medicinal chemistry.

Dr. Letizia Crocetti
Dr. Maris Cinelli
Guest Editors

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Keywords

  • enzyme inhibitors
  • drug design
  • organic synthesis
  • biological evaluation
  • molecular modeling studies
  • kinetic experiment

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Published Papers (4 papers)

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Research

36 pages, 5378 KB  
Article
Discovery of Potent PDE4 Inhibitors with 3(2H)-Pyridazinone Scaffold: Synthesis, In Silico Studies and In Vitro/Vivo Evaluation
by Claudia Vergelli, Letizia Crocetti, Gabriella Guerrini, Fabrizio Melani, Jordi Gracia, Maria Antonia Buil, Yolanda Garrido, Lluis Pagès, Joan Taltavull, Amadeu Gavaldà, Elena Calama and Maria Paola Giovannoni
Molecules 2026, 31(4), 699; https://doi.org/10.3390/molecules31040699 - 17 Feb 2026
Viewed by 233
Abstract
Phospodiesterase 4 (PDE4) has long been an attractive target not only for the anti-inflammatory therapy in respiratory diseases, but also for other pathologies such as psoriatic arthritis and atopic dermatitis. In this study, we report the synthesis of 5-acetyl-2-ethyl-6-phenyl-3(2H)-pyridazinones differently substituted at position [...] Read more.
Phospodiesterase 4 (PDE4) has long been an attractive target not only for the anti-inflammatory therapy in respiratory diseases, but also for other pathologies such as psoriatic arthritis and atopic dermatitis. In this study, we report the synthesis of 5-acetyl-2-ethyl-6-phenyl-3(2H)-pyridazinones differently substituted at position 4 with a variety of aryl/alkylamines, which act as potent PDE4B1 inhibitors in the low nanomolar range. The selectivity toward PDE4A4, PDE4D3 and HARBS, as well as the ability to inhibit TNFα production in human whole blood (hWB), was also evaluated for the most potent products, resulting in a small cluster of compounds with an interesting profile and two selected products (3a and 3k) have been in depth investigated with additional in vitro tests on metabolism and in vivo studies. Finally, molecular docking and minimization of the ligand-enzyme complexes were carried out. Full article
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24 pages, 9675 KB  
Article
N-Aryl-S-aryl-2-mercaptoacetamide Derivatives Effectively Inhibit Mushroom and Cellular Tyrosinase Activities, Melanin Production, and Pigmentation in Zebrafish Larvae: Regarding Copper Ion Chelation
by Hee Jin Jung, Hye Jin Kang, Hyeon Seo Park, Minchang Kim, Hyunju Lee, Hyunhee Ju, Yeonsoo Jeong, Yujin Park, Hae Young Chung and Hyung Ryong Moon
Molecules 2026, 31(3), 422; https://doi.org/10.3390/molecules31030422 - 26 Jan 2026
Viewed by 253
Abstract
In this study, we designed and synthesized 11 N-aryl-S-aryl-2-mercaptoacetamide derivatives as new tyrosinase inhibitors (TYRIs). Experiments with pyrocatechol violet confirmed that four derivatives showed copper-chelating abilities similar to or superior to those of well-known copper-chelating TYRIs like kojic acid (KA) [...] Read more.
In this study, we designed and synthesized 11 N-aryl-S-aryl-2-mercaptoacetamide derivatives as new tyrosinase inhibitors (TYRIs). Experiments with pyrocatechol violet confirmed that four derivatives showed copper-chelating abilities similar to or superior to those of well-known copper-chelating TYRIs like kojic acid (KA) and N-phenylthiourea. However, these four derivatives showed little or no inhibition of mushroom TYR (mTYR) activity and melanin production in B16F10 cells. Instead, derivatives with low copper chelation ability exhibited potent inhibitory effects on mTYR activity and melanin production in B16F10 cells. These findings suggest that the results of metal ion chelation by inhibitors in an enzyme-free environment do not always match those under metalloenzyme conditions because of the interactions between inhibitors and amino acid residues around the metalloenzyme active site. Owing to their favorable interactions with amino acids in the mTYR active site, two of the derivatives inhibited mTYR more effectively than KA. Probably for the same reason, three derivatives inhibited B16F10 cellular TYR more effectively than KA, and one derivative inhibited pigment production in zebrafish larvae much better than KA. This last derivative, which effectively exhibits TYR-inhibitory activity and suppresses melanin production in several species, is considered a promising compound for use as a TYRI in various fields. Full article
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22 pages, 8344 KB  
Article
Discovery of Influenza Neuraminidase Inhibitors: Structure-Based Virtual Screening and Biological Evaluation of Novel Chemotypes
by Rosaria Gitto, Lisa Lombardo, Angela Ravenda, Francesco Broccolo, Antonio Mastino, Laura De Luca and Francesca Marino-Merlo
Molecules 2025, 30(23), 4636; https://doi.org/10.3390/molecules30234636 - 2 Dec 2025
Viewed by 1127
Abstract
Neuraminidase (NA) decorates the surface of the influenza virus, exerting a sialidase activity that enables the viral particle to be released in the host cell. Numerous sialic-based antiviral agents competitively bind to the NA cavity and are marketed worldwide for the treatment of [...] Read more.
Neuraminidase (NA) decorates the surface of the influenza virus, exerting a sialidase activity that enables the viral particle to be released in the host cell. Numerous sialic-based antiviral agents competitively bind to the NA cavity and are marketed worldwide for the treatment of Influenza A infection. We designed and validated a structure-based pharmacophore model for influenza neuraminidase (NA), which guided a virtual screening campaign against an in-house library of compounds already available for testing. This fast and cost-effective in silico strategy resulted in the identification of seven candidates possessing indole or isoquinoline chemical core. In vitro assays confirmed their favorable cytotoxicity profiles and identified only one, the 1-(1H-indol-3-ylcarbonyl)-3-piperidinecarboxylic acid (1), with reproducible inhibitory activity toward NA at non-cytotoxic concentrations. This work suggested a validated workflow for the discovery of novel NA inhibitors and highlighted an indole-based hit compound as a starting point for further optimization. Full article
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17 pages, 3789 KB  
Article
A PI3K Inhibitor with Low Cardiotoxicity and Its Synergistic Inhibitory Effect with Gilteritinib in Acute Myelogenous Leukemia (AML) Cells
by Tianze Wu, Yi Chen, Yimin Gong, Mingzhu Lu, Chengbin Yang, Yannan Yang, Yun Ling and Yaming Zhou
Molecules 2025, 30(11), 2347; https://doi.org/10.3390/molecules30112347 - 27 May 2025
Viewed by 1383
Abstract
N-(2-chloro-5-(3-(pyridin-4-yl)-1H-pyrazolo [3,4-b]pyridin-5-yl)pyridin-3-yl)-4-fluorobenzenesulfonamide, namely, FD274, is a promising 7-azaindazole-based PI3K inhibitor candidate with high antitumor efficacy against acute myeloid leukemia and reduced cardiotoxicity in the zebrafish model. To advance its clinical translation, in this work, we conducted comprehensive assessments of the [...] Read more.
N-(2-chloro-5-(3-(pyridin-4-yl)-1H-pyrazolo [3,4-b]pyridin-5-yl)pyridin-3-yl)-4-fluorobenzenesulfonamide, namely, FD274, is a promising 7-azaindazole-based PI3K inhibitor candidate with high antitumor efficacy against acute myeloid leukemia and reduced cardiotoxicity in the zebrafish model. To advance its clinical translation, in this work, we conducted comprehensive assessments of the cardiotoxicity of FD274 and preliminarily investigated its synergistic antitumor effects with an FLT3 inhibitor, Gilteritinib. The cardiotoxicity profile of FD274, as well as its bioisostere FD268 (positive control), was evaluated using the C57BL/6 mouse model and the H9C2 cell line. The cardiotoxicity of FD274 after a consecutive 20-day treatment period was further assessed in an HL-60 xenograft mouse model. The synergistic cytotoxicity of FD274 with Gilteritinib was evaluated in the HL-60 cell line and the FLT3-ITD cell line MV-4-11. FD274 demonstrated lower adverse effects associated with cardiac dysfunction, oxidative stress, and myocardial injury in the C57BL/6 mouse model and in the H9C2 cell line as compared with FD268. Its negligible adverse effect was further validated in the HL-60 xenograft mice after the 20-day treatment process. Moreover, FD274 demonstrated a synergistic pro-apoptotic effect with Gilteritinib in both HL-60 and MV-4-11 cells. Our findings confirmed the low cardiotoxicity of FD274 and its great potential for combination therapy with Gilteritinib, warranting further development. Full article
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