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Proteases and Their Inhibitors

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: 31 October 2026 | Viewed by 3028

Special Issue Editor


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Guest Editor
Department of Pathology and Immunology, University of Geneva, CH-1201 Geneva, Switzerland
Interests: serine proteases and extracellular proteolysis; inhibitors of serine proteases (SERPINs); protein translocation across membranes; genetics of bacteria and phages

Special Issue Information

Dear Colleagues,

The control of protein homeostasis is essential in all aspects of life. Proteases are present both inside cells and in the extracellular space. The main families of proteases are serine proteases, thiol proteases, acid proteases, and metalloproteases. Serine proteases include digestive enzymes (trypsin, chymotrypsin, etc.) whose enzymatic mechanism is well understood, as well as enzymes of the coagulation and fibrinolytic cascades. More recently, the proteasome of eukaryotes has been shown to play a key role in the cytoplasm. Viral proteases are important targets in therapeutic approaches.

Protease inhibitors are usually classified as low- or high-molecular-weight molecules. Small inhibitors include many natural and synthetic molecules. They are essential tools both in a clinical context and in biochemical experiments. The most well-studied large inhibitors belong to the family of SERPINs (serine protease inhibitors, although several of them also inhibit thiol proteases). However, ovalbumin, a founding member of the SERPINs, is not a known protease inhibitor. Finally, alpha-2-macroglobulins are very large proteins that inhibit many proteases, regardless of their mechanism of action or substrate specificity.

Prof. Dr. Dominique Belin
Guest Editor

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Keywords

  • protease
  • serine proteases
  • thiol proteases
  • acid proteases
  • metalloproteases
  • protease inhibitor
  • SERPINs

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Published Papers (3 papers)

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Research

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17 pages, 3319 KB  
Article
The Role of the Omega Subzone in Determining the Membership of a Protein in One of the Two Families of the LexA/Signal Peptidase-like Superfamily
by Alexander I. Denesyuk, Konstantin Denessiouk, Mark S. Johnson and Vladimir N. Uversky
Int. J. Mol. Sci. 2026, 27(5), 2127; https://doi.org/10.3390/ijms27052127 - 25 Feb 2026
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Abstract
LexA/signal peptidase-like superfamily proteins are serine proteases that use the Ser-Lys catalytic dyad to carry out their biological functions. Here, we investigate the two known families of LexA/signal peptidase-like superfamily proteins, the type I signal peptidase and LexA endopeptidase domain-like, and describe the [...] Read more.
LexA/signal peptidase-like superfamily proteins are serine proteases that use the Ser-Lys catalytic dyad to carry out their biological functions. Here, we investigate the two known families of LexA/signal peptidase-like superfamily proteins, the type I signal peptidase and LexA endopeptidase domain-like, and describe the structural catalytic cores that govern the catalytic residues in these proteins. We show that the structural catalytic core of these proteins is a combination of two subzones, the NucBaseOmega and Omega. While the NucBaseOmega subzone is a pattern observed in all proteins of the studied superfamily, the Omega subzone in the type I signal peptidase family differs from that of the LexA endopeptidase domain-like family. Thus, the amino acids and 3D characteristics of the Omega subzone are a structural marker of the proteins belonging to a specific family. Full article
(This article belongs to the Special Issue Proteases and Their Inhibitors)
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35 pages, 8701 KB  
Article
Design, Synthesis, and Biological Evaluation of Novel Acetylcholinesterase and β-Secretase 1 Inhibitors
by Danuta Drozdowska, Damian Pawelski, Agnieszka Wróbel-Tałałaj, Marta Plonska-Brzezinska, Beata Kolesinska, Ryszard Lazny, Barbara Seroka, Cezary Parzych and Artur Ratkiewicz
Int. J. Mol. Sci. 2026, 27(2), 1008; https://doi.org/10.3390/ijms27021008 - 20 Jan 2026
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Abstract
A series of novel granatane–triazole hybrid molecules was designed, synthesized, and evaluated as dual acetylcholinesterase (AChE) and β-secretase 1 (BACE1) inhibitors. The compounds were obtained through a convergent synthetic route involving azide formation, triazole construction via dipolar cycloaddition, and final coupling with a [...] Read more.
A series of novel granatane–triazole hybrid molecules was designed, synthesized, and evaluated as dual acetylcholinesterase (AChE) and β-secretase 1 (BACE1) inhibitors. The compounds were obtained through a convergent synthetic route involving azide formation, triazole construction via dipolar cycloaddition, and final coupling with a granatane scaffold to give a pseudopelletierine (3-granatanone) analogue. In vitro assays demonstrated that all target compounds inhibited both AChE and BACE1. Molecular docking and molecular dynamics simulations revealed stable interactions with key catalytic residues, suggesting distinct binding modes compared to reference ligands. QSAR-based pharmacokinetic predictions indicated favorable blood–brain barrier permeability and compliance with key drug-likeness filters. These findings identify granatane–triazole hybrids as promising multi-target directed ligand (MTDL) candidates with potential for further optimization in the search for new anti-Alzheimer therapeutics. Full article
(This article belongs to the Special Issue Proteases and Their Inhibitors)
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Review

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39 pages, 1449 KB  
Review
Membrane-Anchored Serine Protease Inhibitors: Physiological Functions, Mechanisms, and Roles in Cancer
by Chun-Ying Chen, Tai-No Lin and Hsiang-Po Huang
Int. J. Mol. Sci. 2026, 27(4), 2000; https://doi.org/10.3390/ijms27042000 - 19 Feb 2026
Cited by 1 | Viewed by 946
Abstract
Pericellular proteolysis is essential for maintaining tissue homeostasis. Central to this process are hepatocyte growth factor activator inhibitor-1 (HAI-1) and HAI-2, membrane-bound inhibitors that regulate type II transmembrane serine proteases, including matriptase and prostasin, through high-affinity Kunitz domains. This review summarizes current understanding [...] Read more.
Pericellular proteolysis is essential for maintaining tissue homeostasis. Central to this process are hepatocyte growth factor activator inhibitor-1 (HAI-1) and HAI-2, membrane-bound inhibitors that regulate type II transmembrane serine proteases, including matriptase and prostasin, through high-affinity Kunitz domains. This review summarizes current understanding of their molecular structures, physiological roles, and cancer-related clinical relevance. Genetic models reveal HAI-1 is critical for placental and skin development, while HAI-2 is crucial for neural tube closure and intestinal integrity. In cancer, HAIs generally act as tumor suppressors. Their downregulation, often via promoter hypermethylation, leads to excessive activation of hepatocyte growth factor/c-MET or protease-activated receptor-2/NF-κB signaling, promoting epithelial–mesenchymal transition and cancer progression. Clinically, reduced HAI levels in tumors correlate with metastasis and poor prognosis in several carcinomas. Paradoxically, elevated HAI expression in certain cancers suggests context-dependent pro-tumor functions. Emerging evidence links HAI loss to immune suppression, notably via M2 macrophage polarization in lung cancer. Finally, we highlight future directions for identifying tissue-specific serine proteases, downstream signaling, and therapeutic strategies, including recombinant mimetics and epigenetic reactivation, in precision oncology. In conclusion, HAI-1 and HAI-2 are key regulators of tissue homeostasis and cancer, with overlapping yet distinct functions, which present promising opportunities for therapeutic targeting. Full article
(This article belongs to the Special Issue Proteases and Their Inhibitors)
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