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Proteases and Their Inhibitors: From Biochemistry to Applications

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

Deadline for manuscript submissions: closed (20 December 2025) | Viewed by 1061

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Guest Editor
College of Dentistry, University of Illinois at Chicago, Chicago, IL 60612, USA
Interests: proteases; serpins; coagulation factors; proprotein convertases; furin; regulation of virus cell entry by proteases
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Special Issue Information

Dear Colleagues,

Proteases or peptidases are a diverse family of enzymes, universally found in all domains of life, that perform peptide bond cleavage. The MEROPS database classification of proteases organizes them into families based on their evolutionary relationships, catalytic mechanisms, and active site residues. This classification currently includes over 250 families, grouped into 7 major catalytic types (serine, cysteine, aspartic, metallo, threonine, glutamic, and mixed- or unknown-mechanism proteases) and organized within approximately 60 clans. Proteases perform their function in pair with their inhibitors, sometimes forming a regulatory network. Medically relevant protease–inhibitor pairs are essential for maintaining physiological homeostasis across processes like coagulation, immune response, tissue remodeling, apoptosis, digestion, and viral replication. The dysregulation of these pairs’ functionality often leads to diseases such as cancer, inflammation, neurodegeneration, and infections. Protease–inhibitor pairs are vital for agriculture, playing roles in plant defense, stress tolerance, crop improvement, and post-harvest management. Leveraging these systems through genetic engineering and biotechnological innovations holds significant promise for sustainable agriculture and enhanced food security. Proteases and their inhibitors are indispensable in molecular sciences due to their critical roles in health, disease, environmental, and industrial applications. Understanding their mechanisms of action and functions in diverse biological systems opens pathways for innovation and advances in biotechnology.

This Special Issue aims to compile a representative and updated survey of examples, showing progress in our understanding and commercial application of proteases and their inhibitors. It invites expert-level contributions describing how proteases and their inhibitors benefit humans and the world’s economy.

Dr. Gonzalo Izaguirre
Guest Editor

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Keywords

  • proteases
  • peptidases
  • proteinases
  • proteolysis
  • hydrolysis
  • enzymes
  • inhibitors
  • biotechnology
  • drug discovery
  • therapeutics

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Published Papers (1 paper)

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Research

20 pages, 4121 KB  
Article
The Allosteric Communication Network in the Activation of Antithrombin by Heparin
by Gonzalo Izaguirre
Int. J. Mol. Sci. 2025, 26(18), 8984; https://doi.org/10.3390/ijms26188984 - 15 Sep 2025
Viewed by 728
Abstract
The allosteric activation of antithrombin (AT) involves a conformational shift from a native, repressed (R) to a heparin-bound, activated (AH) state. Using computational structural analysis, we identified an evolutionarily conserved allosteric communication network (ACN) comprising the residues H120, Y131, and Y166, which undergo [...] Read more.
The allosteric activation of antithrombin (AT) involves a conformational shift from a native, repressed (R) to a heparin-bound, activated (AH) state. Using computational structural analysis, we identified an evolutionarily conserved allosteric communication network (ACN) comprising the residues H120, Y131, and Y166, which undergo key structural displacements during this transition. Site-directed mutagenesis of these residues markedly enhanced AT native reactivity toward FXa and reduced thermal stability, indicating their role in stabilizing the R state. These findings support a three-step “slingshot” model in which the ACN functions as a molecular lock that restrains stored conformational energy, preventing premature activation. Heparin binding disengages this lock, triggering a cascade of structural changes that propagate from the heparin-binding site (HBS) to the reactive center loop (RCL). Additional mutational analyses of residues bridging the β-sheet A (βsA) and the RCL/exosite domains revealed a delicate energetic balance involving the S380 insertion and E381–R197 salt bridge, which collectively tune the activation threshold. Molecular dynamics simulations of ACN mutants further revealed increased flexibility at both HBS and RCL domains, consistent with concerted allosteric coupling. Together, these results provide new mechanistic insights into the structural basis of AT activation and suggest avenues for engineering heparin-independent AT variants. Full article
(This article belongs to the Special Issue Proteases and Their Inhibitors: From Biochemistry to Applications)
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