1
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Hommel K, Kauth AMA, Kirupakaran A, Theisen S, Hayduk M, Niemeyer FC, Beuck C, Zadmard R, Bayer P, Jan Ravoo B, Voskuhl J, Schrader T, Knauer SK. Functional Linkers Support Targeting of Multivalent Tweezers to Taspase1. Chemistry 2024; 30:e202401542. [PMID: 38958349 DOI: 10.1002/chem.202401542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/04/2024]
Abstract
Taspase 1 is a unique protease not only pivotal for embryonic development but also implicated in leukemias and solid tumors. As such, this enzyme is a promising while still challenging therapeutic target, and with its protein structure featuring a flexible loop preceding the active site a versatile model system for drug development. Supramolecular ligands provide a promising complementary approach to traditional small-molecule inhibitors. Recently, the multivalent arrangement of molecular tweezers allowed the successful targeting of Taspase 1's surface loop. With this study we now want to take the next logic step und utilize functional linker systems that not only allow the implementation of novel properties but also engage in protein surface binding. Consequently, we chose two different linker types differing from the original divalent assembly: a backbone with aggregation-induced emission (AIE) properties to enable monitoring of binding and a calix[4]arene scaffold initially pre-positioning the supramolecular binding units. With a series of four AIE-equipped ligands with stepwise increased valency we demonstrated that the functionalized AIE linkers approach ligand binding affinities in the nanomolar range and allow efficient proteolytic inhibition of Taspase 1. Moreover, implementation of the calix[4]arene backbone further enhanced the ligands' inhibitory potential, pointing to a specific linker contribution.
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Affiliation(s)
- Katrin Hommel
- Molecular Biology II, Center of Medical Biotechnology (ZMB) and Center for Nanointegration (CENIDE), University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
| | - Alisa-Maite A Kauth
- Organic Chemistry Institute and Center for Soft Nanoscience, University of Münster, Busso-Peus-Straße 10, 48149, Münster, Germany
| | - Abbna Kirupakaran
- Institute of Organic Chemistry I, Biosupramolecular Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Sebastian Theisen
- Institute of Organic Chemistry I, Biosupramolecular Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Matthias Hayduk
- Faculty of Chemistry (Organic Chemistry II), Center of Medical Biotechnology (ZMB) and Center for Nanointegration (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Felix C Niemeyer
- Institute of Organic Chemistry I, Biosupramolecular Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
| | - Reza Zadmard
- Department of Organic Chemistry, Chemistry and Chemical Engineering Research Center of Iran (CCERCI), P. O. Box 14335-186, Tehran, Iran
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
| | - Bart Jan Ravoo
- Organic Chemistry Institute and Center for Soft Nanoscience, University of Münster, Busso-Peus-Straße 10, 48149, Münster, Germany
| | - Jens Voskuhl
- Faculty of Chemistry (Organic Chemistry II), Center of Medical Biotechnology (ZMB) and Center for Nanointegration (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Thomas Schrader
- Institute of Organic Chemistry I, Biosupramolecular Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Shirley K Knauer
- Molecular Biology II, Center of Medical Biotechnology (ZMB) and Center for Nanointegration (CENIDE), University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
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2
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Yasuda T, Nakajima N, Ogi T, Yanaka T, Tanaka I, Gotoh T, Kagawa W, Sugasawa K, Tajima K. Heavy water inhibits DNA double-strand break repairs and disturbs cellular transcription, presumably via quantum-level mechanisms of kinetic isotope effects on hydrolytic enzyme reactions. PLoS One 2024; 19:e0309689. [PMID: 39361575 PMCID: PMC11449287 DOI: 10.1371/journal.pone.0309689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 08/16/2024] [Indexed: 10/05/2024] Open
Abstract
Heavy water, containing the heavy hydrogen isotope, is toxic to cells, although the underlying mechanism remains incompletely understood. In addition, certain enzymatic proton transfer reactions exhibit kinetic isotope effects attributed to hydrogen isotopes and their temperature dependencies, indicative of quantum tunneling phenomena. However, the correlation between the biological effects of heavy water and the kinetic isotope effects mediated by hydrogen isotopes remains elusive. In this study, we elucidated the kinetic isotope effects arising from hydrogen isotopes of water and their temperature dependencies in vitro, focusing on deacetylation, DNA cleavage, and protein cleavage, which are crucial enzymatic reactions mediated by hydrolysis. Intriguingly, the intracellular isotope effects of heavy water, related to the in vitro kinetic isotope effects, significantly impeded multiple DNA double-strand break repair mechanisms crucial for cell survival. Additionally, heavy water exposure enhanced histone acetylation and associated transcriptional activation in cells, consistent with the in vitro kinetic isotope effects observed in histone deacetylation reactions. Moreover, as observed for the in vitro kinetic isotope effects, the cytotoxic effect on cell proliferation induced by heavy water exhibited temperature-dependency. These findings reveal the substantial impact of heavy water-induced isotope effects on cellular functions governed by hydrolytic enzymatic reactions, potentially mediated by quantum-level mechanisms underlying kinetic isotope effects.
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Affiliation(s)
- Takeshi Yasuda
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Nakako Nakajima
- QST Hospital, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Tomoko Yanaka
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Izumi Tanaka
- Institute for Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Takaya Gotoh
- Department of Health Science, Daito Bunka University, Saitama, Japan
| | - Wataru Kagawa
- Department of Interdisciplinary Science and Engineering, Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, Tokyo, Japan
| | - Kaoru Sugasawa
- Biosignal Research Center, and Graduate School of Science, Kobe University, Kobe, Japan
| | - Katsushi Tajima
- Department of Hematology, Yamagata Prefectural Central Hospital, Yamagata, Japan
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3
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Mahanta PJ, Lhouvum K. Expression and biochemical characterization of the putative insulinase enzyme PF11_0189 found in the Plasmodium falciparum genome. Protein Expr Purif 2024; 222:106539. [PMID: 38960013 DOI: 10.1016/j.pep.2024.106539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/21/2024] [Accepted: 06/30/2024] [Indexed: 07/05/2024]
Abstract
PF11_0189 is a putative insulin degrading enzyme present in Plasmodium falciparum genome. The catalytic domain of PF11_0189 is about 27 kDa. Substrate specificity study shows PF11_0189 acts upon different types of proteins. The substrate specificity is found to be highest when insulin is used as a substrate. Metal dependency study shows highest dependency of PF11_0189 towards zinc metal for its proteolytic activity. Chelation of zinc metal with EDTA shows complete absence of PF11_0189 activity. Peptide inhibitors, P-70 and P-121 from combinatorial peptide library prepared against PF11_0189 show inhibition with an IC50 value of 4.8 μM and 7.5 μM respectively. A proven natural anti-malarial peptide cyclosporin A shows complete inhibition against PF11_0189 with an IC50 value of 0.75 μM suggesting PF11_0189 as a potential target for peptide inhibitors. The study implicates that PF11_0189 is a zinc metalloprotease involved in catalysis of insulin. The study gives a preliminary insight into the mechanism of complications arising from glucose abnormalities during severe malaria.
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Affiliation(s)
- Prabhash Jyoti Mahanta
- Department of Biotechnology, National Institute of Technology, Arunachal Pradesh, India.
| | - Kimjolly Lhouvum
- Department of Biotechnology, National Institute of Technology, Arunachal Pradesh, India
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4
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Lira AL, Kohs TC, Moellmer SA, Shatzel JJ, McCarty OJ, Puy C. Substrates, Cofactors, and Cellular Targets of Coagulation Factor XIa. Semin Thromb Hemost 2024; 50:962-969. [PMID: 36940715 PMCID: PMC11069399 DOI: 10.1055/s-0043-1764469] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2023]
Abstract
Coagulation factor XI (FXI) has increasingly been shown to play an integral role in several physiologic and pathological processes. FXI is among several zymogens within the blood coagulation cascade that are activated by proteolytic cleavage, with FXI converting to the active serine protease form (FXIa). The evolutionary origins of FXI trace back to duplication of the gene that transcribes plasma prekallikrein, a key factor in the plasma kallikrein-kinin system, before further genetic divergence led to FXI playing a unique role in blood coagulation. While FXIa is canonically known for activating the intrinsic pathway of coagulation by catalyzing the conversion of FIX into FIXa, it is promiscuous in nature and has been shown to contribute to thrombin generation independent of FIX. In addition to its role in the intrinsic pathway of coagulation, FXI also interacts with platelets, endothelial cells, and mediates the inflammatory response through activation of FXII and cleavage of high-molecular-weight kininogen to generate bradykinin. In this manuscript, we critically review the current body of knowledge surrounding how FXI navigates the interplay of hemostasis, inflammatory processes, and the immune response and highlight future avenues for research. As FXI continues to be clinically explored as a druggable therapeutic target, understanding how this coagulation factor fits into physiological and disease mechanisms becomes increasingly important.
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Affiliation(s)
- André L. Lira
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Tia C.L. Kohs
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Samantha A. Moellmer
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Joseph J. Shatzel
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, Oregon
- Divison of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Owen J.T. McCarty
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, Oregon
- Divison of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Cristina Puy
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, Oregon
- Divison of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon
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5
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Cao Z, Liu C, Wen J, Lu Y. Innovative Formulation Platform: Paving the Way for Superior Protein Therapeutics with Enhanced Efficacy and Broadened Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2403116. [PMID: 38819929 DOI: 10.1002/adma.202403116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/19/2024] [Indexed: 06/02/2024]
Abstract
Protein therapeutics offer high therapeutic potency and specificity; the broader adoptions and development of protein therapeutics, however, have been constricted by their intrinsic limitations such as inadequate stability, immunogenicity, suboptimal pharmacokinetics and biodistribution, and off-target effects. This review describes a platform technology that formulates individual protein molecules with a thin formulation layer of crosslinked polymers, which confers the protein therapeutics with high activity, enhanced stability, controlled release capability, reduced immunogenicity, improved pharmacokinetics and biodistribution, and ability to cross the blood brain barriers. Based on currently approved protein therapeutics, this formulating platform affords the development of a vast family of superior protein therapeutics with improved efficacy and broadened indications at significantly reduced cost.
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Affiliation(s)
- Zheng Cao
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, 90095, USA
| | - Chaoyong Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Jing Wen
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, UCLA AIDS Institute, University of California, Los Angeles, CA, 90066, USA
| | - Yunfeng Lu
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, 90095, USA
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
- Changping Laboratory, Beijing, 100871, P. R. China
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6
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Paul DC, Bhattacharjee M. Revisiting the significance of natural protease inhibitors: A comprehensive review. Int J Biol Macromol 2024; 280:135899. [PMID: 39317291 DOI: 10.1016/j.ijbiomac.2024.135899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 08/09/2024] [Accepted: 09/20/2024] [Indexed: 09/26/2024]
Abstract
Protease inhibitors (PIs) function as a natural adversary to proteolytic enzymes. They can diminish or inhibit the catalytic properties of proteases, which are crucial for various tasks in the physiology and metabolism of cellular forms. Protease Inhibitors are low molecular weight (5-25 kDa) stable proteins. Plants are a fair source of PIs, so foods containing PIs remarkably influence human health. PIs are usually present in storage tissues of the plant, although they are present in other aerial parts as well. In plants, protease inhibitors participate in vital functions such as maintaining physiological homeostasis, mobilization of storage proteins, defense systems, apoptosis, and other processes. In recent years, plant-derived PIs have shown promising results in treating various diseases including inflammatory conditions, osteoporosis, cardiovascular issues, and brain disorders. The primary goal of this review is to provide a comprehensive understanding of the characteristics, applications, and challenges associated with natural protease inhibitors in plants, which draws insights from an extensive examination of 80+ research papers with a focus on their potential in agriculture and medicine. By synthesizing findings from an extensive literature review, this work aims to guide future research directions and innovations in leveraging plant-based PIs for sustainable agricultural practices and advanced therapeutic interventions.
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Affiliation(s)
- Dhiman Chandra Paul
- Programme of Biotechnology, Assam down town University, Panikhaiti, Gandhinagar, Guwahati, Assam 26, India
| | - Minakshi Bhattacharjee
- Programme of Biotechnology, Assam down town University, Panikhaiti, Gandhinagar, Guwahati, Assam 26, India.
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7
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Turk V, Stoka V. Lysosomal Proteases and Their Inhibitors. Int J Mol Sci 2024; 25:10070. [PMID: 39337555 PMCID: PMC11432586 DOI: 10.3390/ijms251810070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
The discovery of the lysosome, a major cytoplasmic organelle, represents a breakthrough in the understanding of intracellular protein degradation processes-proteolysis [...].
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Affiliation(s)
- Vito Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia
| | - Veronika Stoka
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia
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8
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Kwon S, Andreas MP, Giessen TW. Pore Engineering as a General Strategy to Improve Protein-Based Enzyme Nanoreactor Performance. ACS NANO 2024; 18:25740-25753. [PMID: 39226211 DOI: 10.1021/acsnano.4c08186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Enzyme nanoreactors are nanoscale compartments consisting of encapsulated enzymes and a selectively permeable barrier. Sequestration and colocalization of enzymes can increase catalytic activity, stability, and longevity, highly desirable features for many biotechnological and biomedical applications of enzyme catalysts. One promising strategy to construct enzyme nanoreactors is to repurpose protein nanocages found in nature. However, protein-based enzyme nanoreactors often exhibit decreased catalytic activity, partially caused by a mismatch of protein shell selectivity and the substrate requirements of encapsulated enzymes. No broadly applicable and modular protein-based nanoreactor platform is currently available. Here, we introduce a pore-engineered universal enzyme nanoreactor platform based on encapsulins-microbial self-assembling protein nanocompartments with programmable and selective enzyme packaging capabilities. We structurally characterize our protein shell designs via cryo-electron microscopy and highlight their polymorphic nature. Through fluorescence polarization assays, we show their improved molecular flux behavior and highlight their expanded substrate range via a number of proof-of-concept enzyme nanoreactor designs. This work lays the foundation for utilizing our encapsulin-based nanoreactor platform for diverse future biotechnological and biomedical applications.
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Affiliation(s)
- Seokmu Kwon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Michael P Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
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9
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Khiari Z. Enzymes from Fishery and Aquaculture Waste: Research Trends in the Era of Artificial Intelligence and Circular Bio-Economy. Mar Drugs 2024; 22:411. [PMID: 39330292 PMCID: PMC11433245 DOI: 10.3390/md22090411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 09/06/2024] [Accepted: 09/07/2024] [Indexed: 09/28/2024] Open
Abstract
In the era of the blue bio-economy, which promotes the sustainable utilization and exploitation of marine resources for economic growth and development, the fisheries and aquaculture industries still face huge sustainability issues. One of the major challenges of these industries is associated with the generation and management of wastes, which pose a serious threat to human health and the environment if not properly treated. In the best-case scenario, fishery and aquaculture waste is processed into low-value commodities such as fishmeal and fish oil. However, this renewable organic biomass contains a number of highly valuable bioproducts, including enzymes, bioactive peptides, as well as functional proteins and polysaccharides. Marine-derived enzymes are known to have unique physical, chemical and catalytic characteristics and are reported to be superior to those from plant and animal origins. Moreover, it has been established that enzymes from marine species possess cold-adapted properties, which makes them interesting from technological, economic and sustainability points of view. Therefore, this review centers around enzymes from fishery and aquaculture waste, with a special focus on proteases, lipases, carbohydrases, chitinases and transglutaminases. Additionally, the use of fishery and aquaculture waste as a substrate for the production of industrially relevant microbial enzymes is discussed. The application of emerging technologies (i.e., artificial intelligence and machine learning) in microbial enzyme production is also presented.
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Affiliation(s)
- Zied Khiari
- National Research Council of Canada, Aquatic and Crop Resource Development Research Centre, 1411 Oxford Street, Halifax, NS B3H 3Z1, Canada
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10
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Liu Y, Gilchrist AE, Heilshorn SC. Engineered Protein Hydrogels as Biomimetic Cellular Scaffolds. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2407794. [PMID: 39233559 DOI: 10.1002/adma.202407794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/01/2024] [Indexed: 09/06/2024]
Abstract
The biochemical and biophysical properties of the extracellular matrix (ECM) play a pivotal role in regulating cellular behaviors such as proliferation, migration, and differentiation. Engineered protein-based hydrogels, with highly tunable multifunctional properties, have the potential to replicate key features of the native ECM. Formed by self-assembly or crosslinking, engineered protein-based hydrogels can induce a range of cell behaviors through bioactive and functional domains incorporated into the polymer backbone. Using recombinant techniques, the amino acid sequence of the protein backbone can be designed with precise control over the chain-length, folded structure, and cell-interaction sites. In this review, the modular design of engineered protein-based hydrogels from both a molecular- and network-level perspective are discussed, and summarize recent progress and case studies to highlight the diverse strategies used to construct biomimetic scaffolds. This review focuses on amino acid sequences that form structural blocks, bioactive blocks, and stimuli-responsive blocks designed into the protein backbone for highly precise and tunable control of scaffold properties. Both physical and chemical methods to stabilize dynamic protein networks with defined structure and bioactivity for cell culture applications are discussed. Finally, a discussion of future directions of engineered protein-based hydrogels as biomimetic cellular scaffolds is concluded.
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Affiliation(s)
- Yueming Liu
- Department of Materials Science & Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Aidan E Gilchrist
- Department of Biomedical Engineering, University of California, Davis 451 Health Sciences Dr, GBSF 3315, Davis, CA, 95616, USA
| | - Sarah C Heilshorn
- Department of Materials Science & Engineering, 476 Lomita Mall, McCullough Room 246, Stanford, CA, 94305, USA
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11
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Mótyán JA, Tőzsér J. The human retroviral-like aspartic protease 1 (ASPRV1): From in vitro studies to clinical correlations. J Biol Chem 2024; 300:107634. [PMID: 39098535 PMCID: PMC11402058 DOI: 10.1016/j.jbc.2024.107634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 07/25/2024] [Accepted: 07/27/2024] [Indexed: 08/06/2024] Open
Abstract
The human retroviral-like aspartic protease 1 (ASPRV1) is a retroviral-like protein that was first identified in the skin due to its expression in the stratum granulosum layer of the epidermis. Accordingly, it is also referred to as skin-specific aspartic protease. Similar to the retroviral polyproteins, the full-length ASPRV1 also undergoes self-proteolysis, the processing of the precursor is necessary for the autoactivation of the protease domain. ASPRV1's functions are well-established at the level of the skin: it is part of the epidermal proteolytic network and has a significant contribution to skin moisturization via the limited proteolysis of filaggrin; it is only natural protein substrate identified so far. Filaggrin and ASPRV1 are also specific for mammalians, these proteins provide unique features for the skins of these species, and the importance of filaggrin processing in hydration is proved by the fact that some ASPRV1 mutations are associated with skin diseases such as ichthyosis. ASPRV1 was also found to be expressed in macrophage-like neutrophil cells, indicating that its functions are not limited to the skin. In addition, differential expression of ASPRV1 was detected in many diseases, with yet unknown significance. The currently known enzymatic characteristics-that had been revealed mainly by in vitro studies-and correlations with pathogenic phenotypes imply potentially important functions in multiple cell types, which makes the protein a promising target of functional studies. In this review we describe the currently available knowledge and future perspective in regard to ASPRV1.
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Affiliation(s)
- János András Mótyán
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
| | - József Tőzsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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12
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Petruzzella A, Bruand M, Santamaria-Martínez A, Katanayeva N, Reymond L, Wehrle S, Georgeon S, Inel D, van Dalen FJ, Viertl D, Lau K, Pojer F, Schottelius M, Zoete V, Verdoes M, Arber C, Correia BE, Oricchio E. Antibody-peptide conjugates deliver covalent inhibitors blocking oncogenic cathepsins. Nat Chem Biol 2024; 20:1188-1198. [PMID: 38811854 DOI: 10.1038/s41589-024-01627-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/18/2024] [Indexed: 05/31/2024]
Abstract
Cysteine cathepsins are a family of proteases that are relevant therapeutic targets for the treatment of different cancers and other diseases. However, no clinically approved drugs for these proteins exist, as their systemic inhibition can induce deleterious side effects. To address this problem, we developed a modular antibody-based platform for targeted drug delivery by conjugating non-natural peptide inhibitors (NNPIs) to antibodies. NNPIs were functionalized with reactive warheads for covalent inhibition, optimized with deep saturation mutagenesis and conjugated to antibodies to enable cell-type-specific delivery. Our antibody-peptide inhibitor conjugates specifically blocked the activity of cathepsins in different cancer cells, as well as osteoclasts, and showed therapeutic efficacy in vitro and in vivo. Overall, our approach allows for the rapid design of selective cathepsin inhibitors and can be generalized to inhibit a broad class of proteases in cancer and other diseases.
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Affiliation(s)
- Aaron Petruzzella
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Marine Bruand
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Albert Santamaria-Martínez
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Natalya Katanayeva
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Luc Reymond
- Institute of Chemical Sciences and Engineering (ISIC), Institute of Bioengineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Sarah Wehrle
- Laboratory of Protein Design and Immunoengineering, School of Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Sandrine Georgeon
- Laboratory of Protein Design and Immunoengineering, School of Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Damla Inel
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Floris J van Dalen
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute for Chemical Immunology, Nijmegen, The Netherlands
| | - David Viertl
- Translational Radiopharmaceutical Sciences, Departments of Nuclear Medicine and Molecular Imaging and of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- In Vivo Imaging Facility, Department of Research and Training, University of Lausanne (UNIL), Lausanne, Switzerland
| | - Kelvin Lau
- Protein Production and Structure Core Facility, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Florence Pojer
- Protein Production and Structure Core Facility, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Margret Schottelius
- Translational Radiopharmaceutical Sciences, Departments of Nuclear Medicine and Molecular Imaging and of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- AGORA Pôle de Recherche sur le Cancer, Lausanne, Switzerland
| | - Vincent Zoete
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Martijn Verdoes
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute for Chemical Immunology, Nijmegen, The Netherlands
| | - Caroline Arber
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Bruno E Correia
- Laboratory of Protein Design and Immunoengineering, School of Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
| | - Elisa Oricchio
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland.
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13
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Zhang Y, Lei F, Qian W, Zhang C, Wang Q, Liu C, Ji H, Liu Z, Wang F. Designing intelligent bioorthogonal nanozymes: Recent advances of stimuli-responsive catalytic systems for biomedical applications. J Control Release 2024; 373:929-951. [PMID: 39097195 DOI: 10.1016/j.jconrel.2024.07.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/28/2024] [Accepted: 07/29/2024] [Indexed: 08/05/2024]
Abstract
Bioorthogonal nanozymes have emerged as a potent tool in biomedicine due to their unique ability to perform enzymatic reactions that do not interfere with native biochemical processes. The integration of stimuli-responsive mechanisms into these nanozymes has further expanded their potential, allowing for controlled activation and targeted delivery. As such, intelligent bioorthogonal nanozymes have received more and more attention in developing therapeutic approaches. This review provides a comprehensive overview of the recent advances in the development and application of stimuli-responsive bioorthogonal nanozymes. By summarizing the design outlines for anchoring bioorthogonal nanozymes with stimuli-responsive capability, this review seeks to offer valuable insights and guidance for the rational design of these remarkable materials. This review highlights the significant progress made in this exciting field with different types of stimuli and the various applications. Additionally, it also examines the current challenges and limitations in the design, synthesis, and application of these systems, and proposes potential solutions and research directions. This review aims to stimulate further research toward the development of more efficient and versatile stimuli-responsive bioorthogonal nanozymes for biomedical applications.
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Affiliation(s)
- Yan Zhang
- Institute of Special Environmental Medicine, Nantong University, Nantong 226019, China
| | - Fang Lei
- School of Public Health, Nantong University, Nantong 226019, China
| | - Wanlong Qian
- Institute of Special Environmental Medicine, Nantong University, Nantong 226019, China
| | - Chengfeng Zhang
- Institute of Special Environmental Medicine, Nantong University, Nantong 226019, China
| | - Qi Wang
- School of Public Health, Nantong University, Nantong 226019, China
| | - Chaoqun Liu
- School of Pharmacy, Henan University, Kaifeng 475004, China
| | - Haiwei Ji
- School of Public Health, Nantong University, Nantong 226019, China
| | - Zhengwei Liu
- Precision Immunology Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York 10029, USA.
| | - Faming Wang
- School of Public Health, Nantong University, Nantong 226019, China.
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14
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Chihab A, El Brahmi N, Hamdoun G, El Abbouchi A, Ghammaz H, Touil N, Bousmina M, El Fahime E, El Kazzouli S. Development of a new experimental NMR strategy for covalent cysteine protease inhibitors screening: toward enhanced drug discovery. RSC Adv 2024; 14:26829-26836. [PMID: 39184001 PMCID: PMC11342919 DOI: 10.1039/d4ra04938a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Accepted: 08/13/2024] [Indexed: 08/27/2024] Open
Abstract
In the development of antiviral drugs, proteases and polymerases are among the most important targets. Cysteine proteases, also known as thiol proteases, catalyze the degradation of proteins by cleaving peptide bonds using the nucleophilic thiol group of cysteine. As part of our research, we are examining how cysteine, an essential amino acid found in the active site of the main protease (Mpro) enzyme in SARS-CoV-2, interacts with electrophilic groups present in ethacrynic acid (EA) and compounds 4, 6, and 8 to form sulfur-carbon bonds. Nuclear magnetic resonance (NMR) spectroscopy was used to monitor the reaction rate between cysteine and Michael acceptors. We found that the inhibitory activity of these compounds towards Mpro is correlated to their chemical reactivity toward cysteine. This approach may serve as a valuable tool in drug development for detecting potential covalent inhibitors of Mpro and other cysteine proteases.
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Affiliation(s)
| | | | | | | | - Hamza Ghammaz
- Centre National de la Recherche Scientifique et Technique (CNRST) Angle avenues des FAR et Allal El Fassi, Hay Ryad 10102 Rabat Morocco
| | - Nadia Touil
- Cell Culture Unit, Center of Virology, Infectious, and Tropical Diseases Mohammed V Military Hospital Rabat Morocco
| | | | - Elmostafa El Fahime
- Centre National de la Recherche Scientifique et Technique (CNRST) Angle avenues des FAR et Allal El Fassi, Hay Ryad 10102 Rabat Morocco
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15
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Fatrekar AP, Morajkar RV, Vernekar AA. Expanding limits of artificial enzymes: unprecedented catalysis by an oxidase nanozyme in activating a structural protein for covalent crosslinking and conferring remarkable proteolytic resistance. Chem Sci 2024:d4sc03767g. [PMID: 39176248 PMCID: PMC11337028 DOI: 10.1039/d4sc03767g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 08/07/2024] [Indexed: 08/24/2024] Open
Abstract
Nature has endowed us with some complex enzymes capable of utilizing proteins as their substrates to generate functional proteins through post-translational modification. However, nanozymes' interplay with proteins as substrates is scarce, with their chemistry predominantly established using only small molecule substrates, featuring a significant gap in this area. Due to the huge prospects of nanozymes in biotechnological and therapeutic interventions, studies establishing the unexplored roles of nanozymes in the biological environments and their interplay beyond small molecule substrates warrant immediate attention. In this study, we unveil the unprecedented role of a Mn-based oxidase nanozyme (MnN) in activating a structural protein, collagen, and covalently crosslinking its tyrosine residues with only a trace amount of tannic acid (TA) without compromising its triple-helical structural integrity. While therapeutic applications demand materials prepared from collagen, the current chemical and physical crosslinking of collagen often presents significant challenges such as toxicity, denaturation, or high costs. MnN lucidly accomplishes crosslinking interplay at its 101 facets using oxygen as a co-substrate under mild conditions. This process takes advantage of MnN being active at mild acidic pH where collagen preferentially exists as a soluble triple helix (monomeric form), exposing functionalities and enhancing the crosslinking degree. Importantly, this reaction also confers 100% resistance to collagenase attack on the collagen tendon-derived biological material. The catalyzed TA-tyrosine linkage in the telopeptide region of collagen probably impedes the initial recognition step of collagenase, providing robust protection against its degradative action. Our study not only expands the repertoire of nanozymes' substrates beyond the existing library of small molecules but also establishes a significant step toward designing a gold standard for collagen crosslinking. With biomedical applications demanding biomaterials derived from protein scaffolds with preserved structural integrity, our investigation bridges the gap between nanozymes' chemistry and crosslinking proteins, opening exciting prospects for biomaterial development.
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Affiliation(s)
- Adarsh P Fatrekar
- Inorganic and Physical Chemistry Laboratory, CSIR-Central Leather Research Institute Chennai-600020 Tamil Nadu India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad-201002 India
| | - Rasmi V Morajkar
- Inorganic and Physical Chemistry Laboratory, CSIR-Central Leather Research Institute Chennai-600020 Tamil Nadu India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad-201002 India
| | - Amit A Vernekar
- Inorganic and Physical Chemistry Laboratory, CSIR-Central Leather Research Institute Chennai-600020 Tamil Nadu India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad-201002 India
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16
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Desgagné M, Désilets A, Ferková S, Lepage M, Perreault O, Joushomme A, Lemieux G, Guerrab W, Froehlich U, Comeau C, Sarret P, Leduc R, Boudreault PL. Rational In Silico Design of Selective TMPRSS6 Peptidomimetic Inhibitors via Exploitation of the S2 Subpocket. J Med Chem 2024; 67:12969-12983. [PMID: 39028865 PMCID: PMC11321340 DOI: 10.1021/acs.jmedchem.4c00922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/17/2024] [Accepted: 06/21/2024] [Indexed: 07/21/2024]
Abstract
TMPRSS6 is a potential therapeutic target for the treatment of iron overload due to its role in regulating levels of hepcidin. Although potent TMPRSS6 inhibitors have been previously developed, their lack of specificity requires optimization to avoid potential side effects before pursuing preclinical development with in vivo models. Here, using computer-aided drug design based on a TMPRSS6 homology model, we reveal that the S2 position of TMPRSS6 offers a potential avenue to achieve selectivity against other members of the TTSP family. Accordingly, we synthesized novel peptidomimetic molecules containing lipophilic amino acids at the P2 position to exploit this unexplored pocket. This enabled us to identify TMPRSS6-selective small molecules with low nanomolar affinity. Finally, pharmacokinetic parameters were determined, and a compound was found to be potent in cellulo toward its primary target while retaining TTSP-subtype selectivity and showing no signs of alteration in in vitro TEER experiments.
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Affiliation(s)
- Michael Desgagné
- Department of Pharmacology-Physiology,
Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC J1H 5N4, Canada
| | - Antoine Désilets
- Department of Pharmacology-Physiology,
Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC J1H 5N4, Canada
| | - Sára Ferková
- Department of Pharmacology-Physiology,
Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC J1H 5N4, Canada
| | - Matthieu Lepage
- Department of Pharmacology-Physiology,
Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC J1H 5N4, Canada
| | - Olivier Perreault
- Department of Pharmacology-Physiology,
Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC J1H 5N4, Canada
| | - Alexandre Joushomme
- Department of Pharmacology-Physiology,
Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC J1H 5N4, Canada
| | - Gabriel Lemieux
- Department of Pharmacology-Physiology,
Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC J1H 5N4, Canada
| | - Walid Guerrab
- Department of Pharmacology-Physiology,
Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC J1H 5N4, Canada
| | - Ulrike Froehlich
- Department of Pharmacology-Physiology,
Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC J1H 5N4, Canada
| | - Christian Comeau
- Department of Pharmacology-Physiology,
Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC J1H 5N4, Canada
| | - Philippe Sarret
- Department of Pharmacology-Physiology,
Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC J1H 5N4, Canada
| | - Richard Leduc
- Department of Pharmacology-Physiology,
Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC J1H 5N4, Canada
| | - Pierre-Luc Boudreault
- Department of Pharmacology-Physiology,
Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC J1H 5N4, Canada
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17
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Lockwood TD. Coordination chemistry suggests that independently observed benefits of metformin and Zn 2+ against COVID-19 are not independent. Biometals 2024; 37:983-1022. [PMID: 38578560 PMCID: PMC11255062 DOI: 10.1007/s10534-024-00590-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/12/2024] [Indexed: 04/06/2024]
Abstract
Independent trials indicate that either oral Zn2+ or metformin can separately improve COVID-19 outcomes by approximately 40%. Coordination chemistry predicts a mechanistic relationship and therapeutic synergy. Zn2+ deficit is a known risk factor for both COVID-19 and non-infectious inflammation. Most dietary Zn2+ is not absorbed. Metformin is a naked ligand that presumably increases intestinal Zn2+ bioavailability and active absorption by cation transporters known to transport metformin. Intracellular Zn2+ provides a natural buffer of many protease reactions; the variable "set point" is determined by Zn2+ regulation or availability. A Zn2+-interactive protease network is suggested here. The two viral cysteine proteases are therapeutic targets against COVID-19. Viral and many host proteases are submaximally inhibited by exchangeable cell Zn2+. Inhibition of cysteine proteases can improve COVID-19 outcomes and non-infectious inflammation. Metformin reportedly enhances the natural moderating effect of Zn2+ on bioassayed proteome degradation. Firstly, the dissociable metformin-Zn2+ complex could be actively transported by intestinal cation transporters; thereby creating artificial pathways of absorption and increased body Zn2+ content. Secondly, metformin Zn2+ coordination can create a non-natural protease inhibitor independent of cell Zn2+ content. Moderation of peptidolytic reactions by either or both mechanisms could slow (a) viral multiplication (b) viral invasion and (c) the pathogenic host inflammatory response. These combined actions could allow development of acquired immunity to clear the infection before life-threatening inflammation. Nirmatrelvir (Paxlovid®) opposes COVID-19 by selective inhibition the viral main protease by a Zn2+-independent mechanism. Pending safety evaluation, predictable synergistic benefits of metformin and Zn2+, and perhaps metformin/Zn2+/Paxlovid® co-administration should be investigated.
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Affiliation(s)
- Thomas D Lockwood
- Department Pharmacology and Toxicology, School of Medicine, Wright State University, Dayton, OH, 45435, USA.
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18
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Song B, Wang X, Qin L, Hussain S, Liang W. Brain gliomas: Diagnostic and therapeutic issues and the prospects of drug-targeted nano-delivery technology. Pharmacol Res 2024; 206:107308. [PMID: 39019336 DOI: 10.1016/j.phrs.2024.107308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 07/12/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024]
Abstract
Glioma is the most common intracranial malignant tumor, with severe difficulty in treatment and a low patient survival rate. Due to the heterogeneity and invasiveness of tumors, lack of personalized clinical treatment design, and physiological barriers, it is often difficult to accurately distinguish gliomas, which dramatically affects the subsequent diagnosis, imaging treatment, and prognosis. Fortunately, nano-delivery systems have demonstrated unprecedented capabilities in diagnosing and treating gliomas in recent years. They have been modified and surface modified to efficiently traverse BBB/BBTB, target lesion sites, and intelligently release therapeutic or contrast agents, thereby achieving precise imaging and treatment. In this review, we focus on nano-delivery systems. Firstly, we provide an overview of the standard and emerging diagnostic and treatment technologies for glioma in clinical practice. After induction and analysis, we focus on summarizing the delivery methods of drug delivery systems, the design of nanoparticles, and their new advances in glioma imaging and treatment in recent years. Finally, we discussed the prospects and potential challenges of drug-delivery systems in diagnosing and treating glioma.
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Affiliation(s)
- Baoqin Song
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, National Key Laboratory of Advanced Drug Delivery and Release Systems, Key Laboratory for Biotechnology Drugs of National Health Commission (Shandong Academy of Medical Sciences), Key Lab for Rare & Uncommon Diseases of Shandong Province, Jinan, Shandong 250117, China
| | - Xiu Wang
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, National Key Laboratory of Advanced Drug Delivery and Release Systems, Key Laboratory for Biotechnology Drugs of National Health Commission (Shandong Academy of Medical Sciences), Key Lab for Rare & Uncommon Diseases of Shandong Province, Jinan, Shandong 250117, China.
| | - Lijing Qin
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, National Key Laboratory of Advanced Drug Delivery and Release Systems, Key Laboratory for Biotechnology Drugs of National Health Commission (Shandong Academy of Medical Sciences), Key Lab for Rare & Uncommon Diseases of Shandong Province, Jinan, Shandong 250117, China
| | - Shehbaz Hussain
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, National Key Laboratory of Advanced Drug Delivery and Release Systems, Key Laboratory for Biotechnology Drugs of National Health Commission (Shandong Academy of Medical Sciences), Key Lab for Rare & Uncommon Diseases of Shandong Province, Jinan, Shandong 250117, China
| | - Wanjun Liang
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, National Key Laboratory of Advanced Drug Delivery and Release Systems, Key Laboratory for Biotechnology Drugs of National Health Commission (Shandong Academy of Medical Sciences), Key Lab for Rare & Uncommon Diseases of Shandong Province, Jinan, Shandong 250117, China.
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19
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Nie C, Jeong H, Hyun KA, Park S, Jung HI. Capillary force-driven reverse-Tesla valve structure for microfluidic bioassays. Analyst 2024; 149:4072-4081. [PMID: 38980104 DOI: 10.1039/d4an00601a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Biological assays involve the lysis of biological particles, enzyme reactions, and gene amplification, and require a certain amount of time for completion. Microfluidic chips are regarded as powerful devices for biological assays and in vitro diagnostics; however, they cannot achieve a high mixing efficiency, particularly in some time-consuming biological reactions. Herein, we introduce a microfluidic reverse-Tesla (reTesla) valve structure in which the fluid is affected by vortices and branch flow convergence, resulting in flow retardation and a high degree of mixing. The reTesla is passively operated by a microfluidic capillary force without any pumping facility. Compared with our previously developed micromixers, this innovative pumpless microfluidic chip exhibited high performance, with a mixing efficiency of more than 93%. The versatility of our reTesla chip will play a pivotal role in the study of various biological and chemical reactions.
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Affiliation(s)
- Cheng Nie
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Hyorim Jeong
- The DABOM Inc., 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Kyung-A Hyun
- Korea Electronics Technology Institute (KETI), 25 Saenari-ro Bundang-gu, Seongnam-si, Gyeonggi-do, 13509, Republic of Korea
| | - Sunyoung Park
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
- The DABOM Inc., 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Hyo-Il Jung
- School of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
- The DABOM Inc., 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
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20
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Kolyadko VN, Layzer JM, Perry K, Sullenger BA, Krishnaswamy S. An RNA aptamer exploits exosite-dependent allostery to achieve specific inhibition of coagulation factor IXa. Proc Natl Acad Sci U S A 2024; 121:e2401136121. [PMID: 38985762 PMCID: PMC11260126 DOI: 10.1073/pnas.2401136121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/06/2024] [Indexed: 07/12/2024] Open
Abstract
Hemostasis relies on a reaction network of serine proteases and their cofactors to form a blood clot. Coagulation factor IXa (protease) plays an essential role in hemostasis as evident from the bleeding disease associated with its absence. RNA aptamers specifically targeting individual coagulation factors have potential as anticoagulants and as probes of the relationship between structure and function. Here, we report X-ray structures of human factor IXa without a ligand bound to the active site either in the apo-form or in complex with an inhibitory aptamer specific for factor IXa. The aptamer binds to an exosite in the catalytic domain and allosterically distorts the active site. Our studies reveal a conformational ensemble of IXa states, wherein large movements of Trp215 near the active site drive functional transitions between the closed (aptamer-bound), latent (apo), and open (substrate-bound) states. The latent state of the apo-enzyme may bear on the uniquely poor catalytic activity of IXa compared to other coagulation proteases. The exosite, to which the aptamer binds, has been implicated in binding VIIIa and heparin, both of which regulate IXa function. Our findings reveal the importance of exosite-driven allosteric modulation of IXa function and new strategies to rebalance hemostasis for therapeutic gain.
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Affiliation(s)
- Vladimir N. Kolyadko
- Division of Hematology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | | | - Kay Perry
- Northeastern Collaborative Access Team, Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL60439
| | | | - Sriram Krishnaswamy
- Division of Hematology, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
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21
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Rawale DG, Gupta M, Thakur K, V R, Rai V. Ordered immobilization of serine proteases enabled by a linchpin directed modification platform. Chem Commun (Camb) 2024; 60:7168-7171. [PMID: 38904189 DOI: 10.1039/d4cc02253j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
We report a chemoselective and site-selective precision engineering of lysine in proteases. The mild and physiological reaction conditions keep their auto-degradation under control. Furthermore, it enables single-site ordered immobilization, enhancing protein digestion and peptide mapping efficiency.
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Affiliation(s)
- Dattatraya Gautam Rawale
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, MP, 462 066, India.
| | - Mrityunjay Gupta
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, MP, 462 066, India.
| | - Kalyani Thakur
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, MP, 462 066, India.
| | - Ragendu V
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, MP, 462 066, India.
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, MP, 462 066, India.
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22
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Poddar S, Yu J. Angiotensin-Converting Enzyme and Renin-Inhibitory Activities of Protein Hydrolysates Produced by Alcalase Hydrolysis of Peanut Protein. Int J Mol Sci 2024; 25:7463. [PMID: 39000571 PMCID: PMC11242875 DOI: 10.3390/ijms25137463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024] Open
Abstract
Hypertension is a major controllable risk factor associated with cardiovascular disease (CVD) and overall mortality worldwide. Most people with hypertension must take medications that are effective in blood pressure management but cause many side effects. Thus, it is important to explore safer antihypertensive alternatives to regulate blood pressure. In this study, peanut protein concentrate (PPC) was hydrolyzed with 3-5% Alcalase for 3-10 h. The in vitro angiotensin-converting enzyme (ACE) and renin-inhibitory activities of the resulting peanut protein hydrolysate (PPH) samples and their fractions of different molecular weight ranges were determined as two measures of their antihypertensive potentials. The results show that the crude PPH produced at 4% Alcalase for 6 h of hydrolysis had the highest ACE-inhibitory activity with IC50 being 5.45 mg/mL. The PPH samples produced with 3-5% Alcalase hydrolysis for 6-8 h also displayed substantial renin-inhibitory activities, which is a great advantage over the animal protein-derived bioactive peptides or hydrolysate. Remarkably higher ACE- and renin-inhibitory activities were observed in fractions smaller than 5 kDa with IC50 being 0.85 and 1.78 mg/mL. Hence, the PPH and its small molecular fraction produced under proper Alcalase hydrolysis conditions have great potential to serve as a cost-effective anti-hypertensive ingredient for blood pressure management.
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Affiliation(s)
- Sukanya Poddar
- Food and Nutritional Sciences Program, Department of Family and Consumer Sciences, North Carolina Agricultural and Technical State University, Greensboro, NC 27411, USA
| | - Jianmei Yu
- Food and Nutritional Sciences Program, Department of Family and Consumer Sciences, North Carolina Agricultural and Technical State University, Greensboro, NC 27411, USA
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23
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Rosenbaum D, Saftig P. New insights into the function and pathophysiology of the ectodomain sheddase A Disintegrin And Metalloproteinase 10 (ADAM10). FEBS J 2024; 291:2733-2766. [PMID: 37218105 DOI: 10.1111/febs.16870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/11/2023] [Accepted: 05/19/2023] [Indexed: 05/24/2023]
Abstract
The 'A Disintegrin And Metalloproteinase 10' (ADAM10) has gained considerable attention due to its discovery as an 'α-secretase' involved in the nonamyloidogenic processing of the amyloid precursor protein, thereby possibly preventing the excessive generation of the amyloid beta peptide, which is associated with the pathogenesis of Alzheimer's disease. ADAM10 was found to exert many additional functions, cleaving about 100 different membrane proteins. ADAM10 is involved in many pathophysiological conditions, ranging from cancer and autoimmune disorders to neurodegeneration and inflammation. ADAM10 cleaves its substrates close to the plasma membrane, a process referred to as ectodomain shedding. This is a central step in the modulation of the functions of cell adhesion proteins and cell surface receptors. ADAM10 activity is controlled by transcriptional and post-translational events. The interaction of ADAM10 with tetraspanins and the way they functionally and structurally depend on each other is another topic of interest. In this review, we will summarize findings on how ADAM10 is regulated and what is known about the biology of the protease. We will focus on novel aspects of the molecular biology and pathophysiology of ADAM10 that were previously poorly covered, such as the role of ADAM10 on extracellular vesicles, its contribution to virus entry, and its involvement in cardiac disease, cancer, inflammation, and immune regulation. ADAM10 has emerged as a regulator controlling cell surface proteins during development and in adult life. Its involvement in disease states suggests that ADAM10 may be exploited as a therapeutic target to treat conditions associated with a dysfunctional proteolytic activity.
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Affiliation(s)
- David Rosenbaum
- Institut für Biochemie, Christian-Albrechts-Universität zu Kiel, Germany
| | - Paul Saftig
- Institut für Biochemie, Christian-Albrechts-Universität zu Kiel, Germany
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24
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Jamal GA, Jahangirian E, Hamblin MR, Mirzaei H, Tarrahimofrad H, Alikowsarzadeh N. Proteases, a powerful biochemical tool in the service of medicine, clinical and pharmaceutical. Prep Biochem Biotechnol 2024:1-25. [PMID: 38909284 DOI: 10.1080/10826068.2024.2364234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
Proteases, enzymes that hydrolyze peptide bonds, have various applications in medicine, clinical applications, and pharmaceutical development. They are used in cancer treatment, wound debridement, contact lens cleaning, prion degradation, biofilm removal, and fibrinolytic agents. Proteases are also crucial in cardiovascular disease treatment, emphasizing the need for safe, affordable, and effective fibrinolytic drugs. Proteolytic enzymes and protease biosensors are increasingly used in diagnostic and therapeutic applications. Advanced technologies, such as nanomaterials-based sensors, are being developed to enhance the sensitivity, specificity, and versatility of protease biosensors. These biosensors are becoming effective tools for disease detection due to their precision and rapidity. They can detect extracellular and intracellular proteases, as well as fluorescence-based methods for real-time and label-free detection of virus-related proteases. The active utilization of proteolytic enzymatic biosensors is expected to expand significantly in biomedical research, in-vitro model systems, and drug development. We focused on journal articles and books published in English between 1982 and 2024 for this study.
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Affiliation(s)
- Ghadir A Jamal
- Faculty of Allied Health Sciences, Kuwait University, Kuwait City, Kuwait
| | - Ehsan Jahangirian
- Department of Molecular, Zist Tashkhis Farda Company (tBioDx), Tehran, Iran
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Faculty of Health Science, Laser Research Center, University of Johannesburg, Doornfontein, South Africa
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | | | - Neda Alikowsarzadeh
- Molecular and Life Science Department, Han University of Applied Science, Arnhem, Nederland
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Fayzullin I, Gorbachev A, Volfson S, Serikbayev Y, Nakyp A, Akylbekov N. Composite Material Based on Polypropylene and Modified Natural Fillers. Polymers (Basel) 2024; 16:1703. [PMID: 38932053 PMCID: PMC11207623 DOI: 10.3390/polym16121703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
The work presents the results of a comprehensive study on obtaining compositions based on polypropylene and natural fillers modified by enzymatic preparations under high-shear forces. The experiment protocol includes determining the modification time and the ratio of water volume to the mass of natural filler (hydro modulus) during modification, which turned out to be different for each type of filler. Physical and mechanical analyses were conducted to evaluate the operational characteristics of the obtained composites, with particular attention given to comparing the modified compositions with their unmodified counterparts. The time and hydro module of the enzymatic modification of the natural fillers under consideration were investigated, which turned out to be different for each type of filler. It was found that surface modification of natural fillers improves mechanical properties; namely, the tensile strength of composites with wood and sunflower fillers increases by 10%, and the impact viscosity of composites also increases by 12% with wood and sunflower fillers. Water absorption decreases in composites, after 2 h boiling, with wood flour by 30% and with rice husk by 10%. After a 14-day test at room temperature, water absorption decreases by more than 30% in composites with rice husk. When determining the free surface energy of composites, it was found that the modification of the filler reduces the polarity of the composites in all samples, which can be interpreted as an improvement in the interaction between the filler and the polymer matrix. The findings of this research have important implications for the development of advanced polymeric materials that can be used in a wide range of applications, including automotive, aerospace, and construction industries. The results underscore the importance of surface modifications to optimize the properties of polymeric composites and provide valuable insights into the role of natural fillers in enhancing the performance of these materials.
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Affiliation(s)
- Ilnur Fayzullin
- Institute of Polymers, Kazan National Research Technological University, 68 K. Marx Str., 420015 Kazan, Russia; (A.G.); (S.V.); (A.N.)
| | - Aleksandr Gorbachev
- Institute of Polymers, Kazan National Research Technological University, 68 K. Marx Str., 420015 Kazan, Russia; (A.G.); (S.V.); (A.N.)
| | - Svetoslav Volfson
- Institute of Polymers, Kazan National Research Technological University, 68 K. Marx Str., 420015 Kazan, Russia; (A.G.); (S.V.); (A.N.)
| | - Yerbol Serikbayev
- Laboratory of Engineering Profile “Physical and Chemical Methods of Analysis”, Korkyt Ata Kyzylorda University, 29A, Aiteke bi Str., Kyzylorda 120014, Kazakhstan;
| | - Abdirakym Nakyp
- Institute of Polymers, Kazan National Research Technological University, 68 K. Marx Str., 420015 Kazan, Russia; (A.G.); (S.V.); (A.N.)
| | - Nurgali Akylbekov
- Laboratory of Engineering Profile “Physical and Chemical Methods of Analysis”, Korkyt Ata Kyzylorda University, 29A, Aiteke bi Str., Kyzylorda 120014, Kazakhstan;
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Hamm P, Meinel L, Driessen MD. An Introductory Guide to Protease Sensitive Linker Design Using Matrix Metalloproteinase 13 as an Example. ACS Biomater Sci Eng 2024; 10:3693-3706. [PMID: 38813796 DOI: 10.1021/acsbiomaterials.4c00407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Proteases play a crucial role, not only in physiological, but also in pathological processes, such as cancer, inflammation, arthritis, Alzheimer's, and infections, to name but a few. Their ability to cleave peptides can be harnessed for a broad range of biotechnological purposes. To do this efficiently, it is essential to find an amino acid sequence that meets the necessary requirements, including interdependent factors like specificity, selectivity, cleavage kinetics, or synthetic accessibility. Cleavage sequences from natural substrates of the protease may not be optimal in terms of specificity and selectivity, which is why these frequently require arduous and sometimes unsuccessful optimization such as by iterative exchange of single amino acids. Hence, here we describe the systematic design of protease sensitive linkers (PSLs)─peptide sequences specifically cleaved by a target protease─guided by the mass spectrometry based determination of target protease specific cleavage sites from a proteome-based peptide library. It includes a procedure for identifying bespoke PSL sequences, their optimization, synthesis, and validation and introduces a program that can indicate potential cleavage sites by hundreds of enzymes in any arbitrary amino acid sequence. Thereby, we provide an introduction to PSL design, illustrated by the example of matrix metalloproteinase 13 (MMP13). This introduction can serve as a guide and help to greatly accelerate the development and use of protease-sensitive linkers in diverse applications.
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Affiliation(s)
- Prisca Hamm
- Institute for Pharmacy and Food Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Lorenz Meinel
- Institute for Pharmacy and Food Chemistry, University of Würzburg, 97074 Würzburg, Germany
- Helmholtz-Institute for RNA-Based Infection Research (HIRI), 97070 Würzburg, Germany
| | - Marc D Driessen
- Institute of Molecular Medicine I, Proteome Research, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, 40225 Düsseldorf, Germany
- Department for Oral and Craniomaxillofacial and Plastic Surgery, University Hospital Cologne and Faculty of Medicine, University of Cologne, 50937 Cologne, Germany
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Marathe K, Naik J, Maheshwari V. Synthesis, characterisation and in vitro anticancer activity of conjugated protease inhibitor-silver nanoparticles (AgNPs-PI) against human breast MCF-7 and prostate PC-3 cancer cell lines. Bioprocess Biosyst Eng 2024; 47:931-942. [PMID: 38709274 DOI: 10.1007/s00449-024-03023-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 04/13/2024] [Indexed: 05/07/2024]
Abstract
The conjugated silver nanoparticles using biomolecules have attracted great attention of researchers because physical dimensions and surface chemistry play important roles in toxicity and biocompatibility of AgNPs. Hence, in the current study, synthesis of bio-conjugated AgNPs with protein protease inhibitor (PI) isolated from Streptomyces spp. is reported. UV-visible spectra of PI and AgNPs showed stronger peaks at 280 and 405 nm, confirming the synthesis of conjugated AgNPs-PI. TEM and SEM images of AgNPs-PI showed spherical-shaped nanoparticles with a slight increase in particle size and thin amorphous layer around the surface of silver nanomaterial. Circular dichroism, FT-IR and fluorescence spectral studies confirmed AgNPs-PI conjugation. Conjugated AgNPs-PI showed excellent anticancer potential than AgNPs and protease inhibitor separately on human breast MCF-7 and prostate PC-3 cell lines. The findings revealed that surface modification of AgNPs with protein protease inhibitor stabilised the nanomaterial and increased its anticancer activity.
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Affiliation(s)
- Kiran Marathe
- University Institute of Chemical Technology, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon, 425001, MS, India.
| | - Jitendra Naik
- University Institute of Chemical Technology, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon, 425001, MS, India
| | - Vijay Maheshwari
- School of Life Sciences, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon, 425001, MS, India
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Xu B, Anderson BM, Mountford SJ, Thompson PE, Mintern JD, Edgington-Mitchell LE. Cathepsin X deficiency alters the processing and localisation of cathepsin L and impairs cleavage of a nuclear cathepsin L substrate. Biol Chem 2024; 405:351-365. [PMID: 38410910 DOI: 10.1515/hsz-2023-0355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
Abstract
Proteases function within sophisticated networks. Altering the activity of one protease can have sweeping effects on other proteases, leading to changes in their activity, structure, specificity, localisation, stability, and expression. Using a suite of chemical tools, we investigated the impact of cathepsin X, a lysosomal cysteine protease, on the activity and expression of other cysteine proteases and their inhibitors in dendritic cells. Among all proteases examined, cathepsin X gene deletion specifically altered cathepsin L levels; pro-cathepsin L and its single chain accumulated while the two-chain form was unchanged. This effect was recapitulated by chemical inhibition of cathepsin X, suggesting a dependence on its catalytic activity. We demonstrated that accumulation of pro- and single chain cathepsin L was not due to a lack of direct cleavage by cathepsin X or altered glycosylation, secretion, or mRNA expression but may result from changes in lysosomal oxidative stress or pH. In the absence of active cathepsin X, nuclear cathepsin L and cleavage of the known nuclear cathepsin L substrate, Lamin B1, were diminished. Thus, cathepsin X activity selectively regulates cathepsin L, which has the potential to impact the degree of cathepsin L proteolysis, the nature of substrates that it cleaves, and the location of cleavage.
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Affiliation(s)
- Bangyan Xu
- Department of Biochemistry & Pharmacology, 2281 Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne , Parkville, VIC 3052, Australia
| | - Bethany M Anderson
- Department of Biochemistry & Pharmacology, 2281 Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne , Parkville, VIC 3052, Australia
| | - Simon J Mountford
- Medicinal Chemistry, 2541 Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia
| | - Philip E Thompson
- Medicinal Chemistry, 2541 Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia
| | - Justine D Mintern
- Department of Biochemistry & Pharmacology, 2281 Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne , Parkville, VIC 3052, Australia
| | - Laura E Edgington-Mitchell
- Department of Biochemistry & Pharmacology, 2281 Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne , Parkville, VIC 3052, Australia
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29
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Abdel-Mawgod S, Zanaty A, Elhusseiny M, Said D, Samir A, Elsayed MM, Mahana O, Said M, Hussein AM, Hassan HM, Selim A, Shahien MA, Selim K. Genetic heterogeneity of chicken anemia virus isolated in selected Egyptian provinces as a preliminary investigation. Front Vet Sci 2024; 11:1362219. [PMID: 38840626 PMCID: PMC11150715 DOI: 10.3389/fvets.2024.1362219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/29/2024] [Indexed: 06/07/2024] Open
Abstract
Chicken anemia virus (CAV) is a widespread and economically significant pathogen in the poultry industry. In this study 110 samples were collected from various poultry farms in selected Egyptian provinces during 2021-2022 and were tested against CAV by Polymerase Chain Reaction (PCR), revealing 22 positive samples with 20% incidence rate. Full sequence analysis of five selected CAV strains revealed genetic variations in VP1, VP2, and VP3 genes. Phylogenetic analysis grouped the Egyptian strains with reference viruses, mainly in group II, while vaccines like Del-Rose were categorized in group III. Recombination events were detected between an Egyptian strain (genotype II) and the Del-Rose vaccine strain (genotype III), indicating potential recombination between live vaccine strains and field isolates. To evaluate pathogenicity, one Egyptian isolate (F883-2022 CAV) and Del-Rose vaccine were tested in Specific Pathogen Free (SPF) chicks. Chicks in the positive group displayed clinical symptoms, including weakness and stunted growth, with postmortem findings consistent with CAV infection. The vaccine group showed milder symptoms and less severe postmortem changes. This study provides important insights into the genetic diversity of CAV in selected Egyptian poultry farms showing recombination event between field strain and vaccine strains, highlighting the need for advanced vaccination programs, especially for broilers.
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Affiliation(s)
- Sara Abdel-Mawgod
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Ali Zanaty
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Mohamed Elhusseiny
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Dalia Said
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Abdelhafez Samir
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Moataz M. Elsayed
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Osama Mahana
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Mahmoud Said
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Ahmed M. Hussein
- Division of Pharmacology and Toxicology, Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Heba M. Hassan
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Abdullah Selim
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Momtaz A. Shahien
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Karim Selim
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
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30
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Haak W, Jagt JZ, de Meij TGJ, Bikker FJ, Brand HS, de Boer NKH, Kaman WE. Fecal proteolytic profiling of pediatric inflammatory bowel disease: A pilot study. FASEB J 2024; 38:e23627. [PMID: 38690708 DOI: 10.1096/fj.202302190r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/18/2024] [Accepted: 04/11/2024] [Indexed: 05/02/2024]
Abstract
Colonoscopy is the gold standard for diagnosing inflammatory bowel disease (IBD). However, this invasive procedure has a high burden for pediatric patients. Previous research has shown elevated fecal amino acid concentrations in children with IBD versus controls. We hypothesized that this finding could result from increased proteolytic activity. Therefore, the aim of this study was to investigate whether fecal protease-based profiling was able to discriminate between IBD and controls. Protease activity was measured in fecal samples from patients with IBD (Crohn's disease (CD) n = 19; ulcerative colitis (UC) n = 19) and non-IBD controls (n = 19) using a fluorescence resonance energy transfer (FRET)-peptide library. Receiver operating characteristic (ROC) curve analysis was used to determine the diagnostic value of each FRET-peptide substrate. Screening the FRET-peptide library revealed an increased total proteolytic activity (TPA), as well as degradation of specific FRET-peptides specifically in fecal samples from IBD patients. Based on level of significance (p < .001) and ROC curve analysis (AUC > 0.85), the fluorogenic substrates W-W, A-A, a-a, F-h, and H-y showed diagnostic potential for CD. The substrates W-W, a-a, T-t, G-v, and H-y showed diagnostic potential for UC based on significance (p < .001) and ROC analysis (AUC > 0.90). None of the FRET-peptide substrates used was able to differentiate between protease activity in fecal samples from CD versus UC. This study showed an increased fecal proteolytic activity in children with newly diagnosed, treatment-naïve, IBD. This could lead to the development of novel, noninvasive biomarkers for screening and diagnostic purposes.
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Affiliation(s)
- Wieke Haak
- Department of Oral Biochemistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
| | - Jasmijn Z Jagt
- Department of Pediatric Gastroenterology, Emma Children's Hospital, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Tim G J de Meij
- Department of Pediatric Gastroenterology, Emma Children's Hospital, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Pediatric Gastroenterology, Emma Children's Hospital, Amsterdam UMC, Academic Medical Centre, Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Floris J Bikker
- Department of Oral Biochemistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
| | - Henk S Brand
- Department of Oral Biochemistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
| | - Nanne K H de Boer
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Wendy E Kaman
- Department of Oral Biochemistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
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Elaine Mankge M, Penistacia Maela M, Mark Abrahams A, Hope Serepa-Dlamini M. Screening of Bacillus spp. bacterial endophytes for protease production, and application in feather degradation and bio-detergent additive. Heliyon 2024; 10:e30736. [PMID: 38765083 PMCID: PMC11098850 DOI: 10.1016/j.heliyon.2024.e30736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Abstract
Research on proteases and secondary metabolites from endophytes is an area that requires attention from researchers. In this study, proteases from Bacillus sp. strain MHSD16 and Bacillus sp. strain MHSD17 endophytes were characterised, and their potential biotechnological applications were investigated. Optimum protease production was achieved when isolates were grown in media containing (g/L): glucose 10g, casein 5g, yeast extract 5g, KH2PO4 2g, Na2CO3 10g at pH 9. The crude protease extracts were active in alkaline environments, thus referred to as alkaline proteases with optimal pH of 10. Additionally, Bacillus sp. strain MHSD 16 and Bacillus sp. strain MHSD17 proteases were active at high temperatures, with optimum enzyme activity at 50 °C. Thermostability profiles of these proteases showed that the enzymes were highly stable between (40-60 °C), maintaining over 85 % stability after 120 min incubation at 60 °C. Furthermore, the enzymes were stable and compatible with various household and laundry detergents. In the presence of commercial laundry detergent, OMO® 68 % and 72 % activity was retained for Bacillus sp. strain MHSD16 and Bacillus sp. strain MHSD17, respectively, while 67 % and 68 % activity were retained in the presence of Sunlight®. The potential application for use in detergents was investigated through the removal of blood stains with the crude alkaline extracts displaying efficient stain removal abilities. Feather degradation was also investigated and Bacillus sp. MHSD17 exhibited feather keratin degrading properties more effectively than Bacillus sp. MHSD16.
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Affiliation(s)
- Malese Elaine Mankge
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, PO Box 17011, Doornfontein, Johannesburg, 2028, South Africa
| | - Mehabo Penistacia Maela
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, PO Box 17011, Doornfontein, Johannesburg, 2028, South Africa
| | - Adrian Mark Abrahams
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, PO Box 17011, Doornfontein, Johannesburg, 2028, South Africa
| | - Mahloro Hope Serepa-Dlamini
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, PO Box 17011, Doornfontein, Johannesburg, 2028, South Africa
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Kwon S, Andreas MP, Giessen TW. Pore engineering as a general strategy to improve protein-based enzyme nanoreactor performance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.02.592161. [PMID: 38746127 PMCID: PMC11092584 DOI: 10.1101/2024.05.02.592161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Enzyme nanoreactors are nanoscale compartments consisting of encapsulated enzymes and a selectively permeable barrier. Sequestration and co-localization of enzymes can increase catalytic activity, stability, and longevity, highly desirable features for many biotechnological and biomedical applications of enzyme catalysts. One promising strategy to construct enzyme nanoreactors is to repurpose protein nanocages found in nature. However, protein-based enzyme nanoreactors often exhibit decreased catalytic activity, partially caused by a mismatch of protein shell selectivity and the substrate requirements of encapsulated enzymes. No broadly applicable and modular protein-based nanoreactor platform is currently available. Here, we introduce a pore-engineered universal enzyme nanoreactor platform based on encapsulins - microbial self-assembling protein nanocompartments with programmable and selective enzyme packaging capabilities. We structurally characterize our protein shell designs via cryo-electron microscopy and highlight their polymorphic nature. Through fluorescence polarization assays, we show their improved molecular flux behavior and highlight their expanded substrate range via a number of proof-of-concept enzyme nanoreactor designs. This work lays the foundation for utilizing our encapsulin-based nanoreactor platform for future biotechnological and biomedical applications.
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Affiliation(s)
- Seokmu Kwon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
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Pečar Fonović U, Kos J, Mitrović A. Compensational role between cathepsins. Biochimie 2024:S0300-9084(24)00085-3. [PMID: 38663456 DOI: 10.1016/j.biochi.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/03/2024] [Accepted: 04/22/2024] [Indexed: 04/30/2024]
Abstract
Cathepsins, a family of lysosomal peptidases, play a crucial role in maintaining cellular homeostasis by regulating protein turnover and degradation as well as many specific regulatory actions that are important for proper cell function and human health. Alterations in the activity and expression of cathepsins have been observed in many diseases such as cancer, inflammation, neurodegenerative disorders, bone remodelling-related conditions and others. These changes are not exclusively harmful, but rather appear to be a compensatory response on the lack of one cathepsin in order to maintain tissue integrity. The upregulation of specific cathepsins in response to the inhibition or dysfunction of other cathepsins suggests a fine-tuned system of proteolytic balance and understanding the compensatory role of cathepsins may improve therapeutic potential of cathepsin's inhibitors. Selectively targeting one cathepsin or modulating their activity could offer new treatment strategies for a number of diseases. This review emphasises the need for comprehensive research into cathepsin biology in the context of disease. The identification of the specific cathepsins involved in compensatory responses, the elucidation of the underlying molecular mechanisms and the development of targeted interventions could lead to innovative therapeutic approaches.
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Affiliation(s)
- Urša Pečar Fonović
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000, Ljubljana, Slovenia.
| | - Janko Kos
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000, Ljubljana, Slovenia; Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia.
| | - Ana Mitrović
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva Cesta 7, 1000, Ljubljana, Slovenia; Department of Biotechnology, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia.
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Devoy C, Flores Bueso Y, Buckley S, Walker S, Tangney M. Synthetic protein protease sensor platform. Front Bioeng Biotechnol 2024; 12:1347953. [PMID: 38646011 PMCID: PMC11026627 DOI: 10.3389/fbioe.2024.1347953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/21/2024] [Indexed: 04/23/2024] Open
Abstract
Introduction: Protease activity can serve as a highly specific biomarker for application in health, biotech, and beyond. The aim of this study was to develop a protease cleavable synthetic protein platform to detect protease activity in a rapid cell-free setting. Methods: The protease sensor is modular, with orthogonal peptide tags at the N and C terminal ends, which can be uncoupled via a protease responsive module located in between. The sensor design allows for several different readouts of cleavage signal. A protein 'backbone' [Green fluorescent protein (GFP)] was designed in silico to have both a C-terminal Flag-tag and N-Terminal 6x histidine tag (HIS) for antibody detection. A protease cleavage site, which can be adapted for any known protease cleavage sequence, enables the uncoupling of the peptide tags. Three different proteases-Tobacco, Etch Virus (TEV), the main protease from coronavirus SARS-COV-2 (Mpro) and Matrix Metallopeptidase 9 (MMP9)-a cancer-selective human protease-were examined. A sandwich Enzyme-Linked Immunosorbent Assay (ELISA) was developed based on antibodies against the HIS and Flag tags. As an alternative readout, a C-terminal quencher peptide separable by protease cleavage from the GFP was also included. Purified proteins were deployed in cell-free cleavage assays with their respective protease. Western blots, fluorescence assays and immunoassay were performed on samples. Results: Following the design, build and validation of protein constructs, specific protease cleavage was initially demonstrated by Western blot. The novel ELISA proved to afford highly sensitive detection of protease activity in all cases. By way of alternative readout, activation of fluorescence signal upon protease cleavage was also demonstrated but did not match the sensitivity provided by the ELISA method. Discussion: This platform, comprising a protease-responsive synthetic protein device and accompanying readout, is suitable for future deployment in a rapid, low-cost, lateral flow setting. The modular protein device can readily accommodate any desired protease-response module (target protease cleavage site). This study validates the concept with three disparate proteases and applications-human infectious disease, cancer and agricultural crop infection.
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Affiliation(s)
- Ciaran Devoy
- Cancer Research@UCC, University College Cork, Cork, Ireland
| | - Yensi Flores Bueso
- Cancer Research@UCC, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Sidney Walker
- Cancer Research@UCC, University College Cork, Cork, Ireland
| | - Mark Tangney
- Cancer Research@UCC, University College Cork, Cork, Ireland
- IEd Hub, University College Cork, Cork, Ireland
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Cigalotto L, Martinvalet D. Granzymes in health and diseases: the good, the bad and the ugly. Front Immunol 2024; 15:1371743. [PMID: 38646541 PMCID: PMC11026543 DOI: 10.3389/fimmu.2024.1371743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
Granzymes are a family of serine proteases, composed of five human members: GA, B, H, M and K. They were first discovered in the 1980s within cytotoxic granules released during NK cell- and T cell-mediated killing. Through their various proteolytic activities, granzymes can trigger different pathways within cells, all of which ultimately lead to the same result, cell death. Over the years, the initial consideration of granzymes as mere cytotoxic mediators has changed due to surprising findings demonstrating their expression in cells other than immune effectors as well as new intracellular and extracellular activities. Additional roles have been identified in the extracellular milieu, following granzyme escape from the immunological synapse or their release by specific cell types. Outside the cell, granzyme activities mediate extracellular matrix alteration via the degradation of matrix proteins or surface receptors. In certain contexts, these processes are essential for tissue homeostasis; in others, excessive matrix degradation and extensive cell death contribute to the onset of chronic diseases, inflammation, and autoimmunity. Here, we provide an overview of both the physiological and pathological roles of granzymes, highlighting their utility while also recognizing how their unregulated presence can trigger the development and/or worsening of diseases.
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Affiliation(s)
- Lavinia Cigalotto
- Laboratory of Reactive Oxygen Species and Cytotoxic Immunity, Department Biomedical Sciences, University of Padova, Padova, Italy
- Veneto Institute Of Molecular Medicine (VIMM), Padova, Italy
| | - Denis Martinvalet
- Laboratory of Reactive Oxygen Species and Cytotoxic Immunity, Department Biomedical Sciences, University of Padova, Padova, Italy
- Veneto Institute Of Molecular Medicine (VIMM), Padova, Italy
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36
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Bhat SY. Drug targeting of aminopeptidases: importance of deploying a right metal cofactor. Biophys Rev 2024; 16:249-256. [PMID: 38737204 PMCID: PMC11078913 DOI: 10.1007/s12551-024-01192-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 05/05/2022] [Indexed: 05/14/2024] Open
Abstract
Aminopeptidases are metal co-factor-dependent hydrolases releasing N-terminal amino acid residues from peptides. Many of these enzymes, particularly the M24 methionine aminopeptidases (MetAPs), are considered valid drug targets in the fight against many parasitic and non-parasitic diseases. Targeting MetAPs has shown promising results against the malarial parasite, Plasmodium, which is regarded as potential anti-cancer targets. While targeting these essential enzymes represents a potentially promising approach, many challenges are often ignored by scientists when designing drugs or inhibitory scaffolds against the MetAPs. One such aspect is the metal co-factor, with inadequate attention paid to its role in catalysis, folding and remodeling of the catalytic site, and its role in inhibitor binding or potency. Knowing that a metal co-factor is essential for aminopeptidase enzyme activity and active site remodeling, it is intriguing that most computational biologists often ignore the metal ion while screening millions of potential inhibitors to find hits. Ironically, a similar trend is followed by biologists who avoid metal promiscuity of these enzymes while screening inhibitor libraries in vitro which may lead to false positives. This review highlights the importance of considering a physiologically relevant metal co-factor during the drug discovery processes targeting metal-dependent aminopeptidases. Graphical abstract
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37
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Zhang H, Wu Y, Zhu Y, Ge L, Huang J, Qin Z. Identification and functional analysis of a serine protease inhibitor using machine learning strategy. Int J Biol Macromol 2024; 265:130852. [PMID: 38508547 DOI: 10.1016/j.ijbiomac.2024.130852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/03/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
In the intricate realm of animal biology, a multitude of vital processes heavily rely on precisely orchestrated proteinase cascades, but the potential for havoc makes proteinase inhibitors indispensable, with serine proteinase inhibitors (serpins) at the forefront, serving as custodians of homeostasis and participating in various critical biological processes. Importantly, there are still many unexplored facets of serpin functionality. In this study, we focused on the serpin family proteins from Marsupenaeus japonicus, utilizing a fine-tuned pretrained protein language model. This approach led to the identification and evolutionary validation of 28 serpins, one of which, referred to as Mjserpin-1, was both computationally and experimentally demonstrated to show potential as an antiviral and apoptosis inhibitor. Our research unveils exciting prospects for the fusion of state-of-the-art artificial intelligence and rich bioinformatics, holding the promise of significant discoveries that could pave the way for future therapeutic advancements.
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Affiliation(s)
- Heqian Zhang
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China.
| | - Yaxin Wu
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China
| | - Yanran Zhu
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China
| | - Liangjun Ge
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China
| | - Jiaquan Huang
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China.
| | - Zhiwei Qin
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China.
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Prange CJ, Sayed NYB, Feng B, Goepfert C, Trujillo DO, Hu X, Tang L. A redox-responsive prodrug for tumor-targeted glutamine restriction. J Control Release 2024; 368:251-264. [PMID: 38403173 DOI: 10.1016/j.jconrel.2024.02.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 02/06/2024] [Accepted: 02/21/2024] [Indexed: 02/27/2024]
Abstract
Modulating the metabolism of cancer cells, immune cells, or both is a promising strategy to potentiate cancer immunotherapy in the nutrient-competitive tumor microenvironment. Glutamine has emerged as an ideal target as cancer cells highly rely on glutamine for replenishing the tricarboxylic acid cycle in the process of aerobic glycolysis. However, non-specific glutamine restriction may induce adverse effects in unconcerned tissues and therefore glutamine inhibitors have achieved limited success in the clinic so far. Here we report the synthesis and evaluation of a redox-responsive prodrug of 6-Diazo-5-oxo-L-norleucine (redox-DON) for tumor-targeted glutamine inhibition. When applied to treat mice bearing subcutaneous CT26 mouse colon carcinoma, redox-DON exhibited equivalent antitumor efficacy but a greatly improved safety profile, particularly, in spleen and gastrointestinal tract, as compared to the state-of-the-art DON prodrug, JHU083. Furthermore, redox-DON synergized with checkpoint blockade antibodies leading to durable cures in tumor-bearing mice. Our results suggest that redox-DON is a safe and effective therapeutic for tumor-targeted glutamine inhibition showing promise for enhanced metabolic modulatory immunotherapy. The approach of reversible chemical modification may be generalized to other metabolic modulatory drugs that suffer from overt toxicity.
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Affiliation(s)
- Céline Jasmin Prange
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland; Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Nadia Yasmina Ben Sayed
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland; Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Bing Feng
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland; Institute of Materials Science & Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Christine Goepfert
- Histology Core Facility, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland; COMPATH, Institute of Veterinary Pathology, University of Berne, Berne CH-3012, Switzerland
| | - Daniel Ortiz Trujillo
- Mass Spectrometry Platform, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Xile Hu
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland.
| | - Li Tang
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland; Institute of Materials Science & Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland.
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Nwamekang Belinga L, Espourteille J, Wepnyu Njamnshi Y, Zafack Zeukang A, Rouaud O, Kongnyu Njamnshi A, Allali G, Richetin K. Circulating Biomarkers for Alzheimer's Disease: Unlocking the Diagnostic Potential in Low- and Middle-Income Countries, Focusing on Africa. NEURODEGENER DIS 2024; 24:26-40. [PMID: 38555638 PMCID: PMC11251669 DOI: 10.1159/000538623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/28/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is emerging as a significant public health challenge in Africa, with predictions indicating a tripling in incidence by 2050. The diagnosis of AD on the African continent is notably difficult, leading to late detection that severely limits treatment options and significantly impacts the quality of life for patients and their families. SUMMARY This review focuses on the potential of high-sensitivity specific blood biomarkers as promising tools for improving AD diagnosis and management globally, particularly in Africa. These advances are particularly pertinent in the continent, where access to medical and technical resources is often limited. KEY MESSAGES Identifying precise, sensitive, and specific blood biomarkers could contribute to the biological characterization and management of AD in Africa. Such advances promise to improve patient care and pave the way for new regional opportunities in pharmaceutical research and drug trials on the continent for AD.
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Affiliation(s)
- Luc Nwamekang Belinga
- Department of Psychiatry, Center for Psychiatric Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Leenaards Memory Center, Department of Clinical Neurosciences, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
- Department of Translational Neuroscience, Brain Research Africa Initiative (BRAIN), Geneva, Switzerland
- Department of Translational Neuroscience, Brain Research Africa Initiative (BRAIN), Yaoundé, Cameroon
| | - Jeanne Espourteille
- Department of Psychiatry, Center for Psychiatric Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Yembe Wepnyu Njamnshi
- Department of Translational Neuroscience, Brain Research Africa Initiative (BRAIN), Geneva, Switzerland
- Department of Translational Neuroscience, Brain Research Africa Initiative (BRAIN), Yaoundé, Cameroon
- Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
- Division of Health Operations Research, Ministry of Public Health, Yaoundé, Cameroon
| | - Ariole Zafack Zeukang
- Department of Translational Neuroscience, Brain Research Africa Initiative (BRAIN), Geneva, Switzerland
- Department of Translational Neuroscience, Brain Research Africa Initiative (BRAIN), Yaoundé, Cameroon
| | - Olivier Rouaud
- Leenaards Memory Center, Department of Clinical Neurosciences, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Alfred Kongnyu Njamnshi
- Department of Translational Neuroscience, Brain Research Africa Initiative (BRAIN), Geneva, Switzerland
- Department of Translational Neuroscience, Brain Research Africa Initiative (BRAIN), Yaoundé, Cameroon
- Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
- Department of Clinical Neuroscience and Neurology, Yaoundé Central Hospital, Yaoundé, Cameroon
| | - Gilles Allali
- Leenaards Memory Center, Department of Clinical Neurosciences, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Kevin Richetin
- Department of Psychiatry, Center for Psychiatric Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Leenaards Memory Center, Department of Clinical Neurosciences, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
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Sharma A, Verwilst P, Li M, Ma D, Singh N, Yoo J, Kim Y, Yang Y, Zhu JH, Huang H, Hu XL, He XP, Zeng L, James TD, Peng X, Sessler JL, Kim JS. Theranostic Fluorescent Probes. Chem Rev 2024; 124:2699-2804. [PMID: 38422393 PMCID: PMC11132561 DOI: 10.1021/acs.chemrev.3c00778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/31/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
The ability to gain spatiotemporal information, and in some cases achieve spatiotemporal control, in the context of drug delivery makes theranostic fluorescent probes an attractive and intensely investigated research topic. This interest is reflected in the steep rise in publications on the topic that have appeared over the past decade. Theranostic fluorescent probes, in their various incarnations, generally comprise a fluorophore linked to a masked drug, in which the drug is released as the result of certain stimuli, with both intrinsic and extrinsic stimuli being reported. This release is then signaled by the emergence of a fluorescent signal. Importantly, the use of appropriate fluorophores has enabled not only this emerging fluorescence as a spatiotemporal marker for drug delivery but also has provided modalities useful in photodynamic, photothermal, and sonodynamic therapeutic applications. In this review we highlight recent work on theranostic fluorescent probes with a particular focus on probes that are activated in tumor microenvironments. We also summarize efforts to develop probes for other applications, such as neurodegenerative diseases and antibacterials. This review celebrates the diversity of designs reported to date, from discrete small-molecule systems to nanomaterials. Our aim is to provide insights into the potential clinical impact of this still-emerging research direction.
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Affiliation(s)
- Amit Sharma
- Amity
School of Chemical Sciences, Amity University
Punjab, Sector 82A, Mohali 140 306, India
| | - Peter Verwilst
- Rega
Institute for Medical Research, Medicinal Chemistry, KU Leuven, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Mingle Li
- College
of Materials Science and Engineering, Shenzhen
University, Shenzhen 518060, China
| | - Dandan Ma
- College
of Materials Science and Engineering, Shenzhen
University, Shenzhen 518060, China
- College
of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Nem Singh
- Department
of Chemistry, Korea University, Seoul 02841, Korea
| | - Jiyoung Yoo
- Department
of Chemistry, Korea University, Seoul 02841, Korea
| | - Yujin Kim
- Department
of Chemistry, Korea University, Seoul 02841, Korea
| | - Ying Yang
- School of
Light Industry and Food Engineering, Guangxi
University, Nanning, Guangxi 530004, China
| | - Jing-Hui Zhu
- College
of Materials Science and Engineering, Shenzhen
University, Shenzhen 518060, China
- College
of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Haiqiao Huang
- College
of Materials Science and Engineering, Shenzhen
University, Shenzhen 518060, China
- College
of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Xi-Le Hu
- Key
Laboratory for Advanced Materials and Joint International Research
Laboratory of Precision Chemistry and Molecular Engineering, Feringa
Nobel Prize Scientist Joint Research Center, School of Chemistry and
Molecular Engineering, East China University
of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xiao-Peng He
- Key
Laboratory for Advanced Materials and Joint International Research
Laboratory of Precision Chemistry and Molecular Engineering, Feringa
Nobel Prize Scientist Joint Research Center, School of Chemistry and
Molecular Engineering, East China University
of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- National
Center for Liver Cancer, the International Cooperation Laboratory
on Signal Transduction, Eastern Hepatobiliary
Surgery Hospital, Shanghai 200438, China
| | - Lintao Zeng
- School of
Light Industry and Food Engineering, Guangxi
University, Nanning, Guangxi 530004, China
| | - Tony D. James
- Department
of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom
- School
of Chemistry and Chemical Engineering, Henan
Normal University, Xinxiang 453007, China
| | - Xiaojun Peng
- College
of Materials Science and Engineering, Shenzhen
University, Shenzhen 518060, China
- State
Key Laboratory of Fine Chemicals, Dalian
University of Technology, Dalian 116024, China
| | - Jonathan L. Sessler
- Department
of Chemistry, The University of Texas at
Austin, Texas 78712-1224, United
States
| | - Jong Seung Kim
- Department
of Chemistry, Korea University, Seoul 02841, Korea
- TheranoChem Incorporation, Seongbuk-gu, Seoul 02841, Korea
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41
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Hou JJ, Ding L, Yang T, Yang YF, Jin YP, Zhang XP, Ma AH, Qin YH. The proteolytic activity in inflammatory bowel disease: insight from gut microbiota. Microb Pathog 2024; 188:106560. [PMID: 38272327 DOI: 10.1016/j.micpath.2024.106560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 01/27/2024]
Abstract
Inflammatory bowel disease (IBD) is a chronic, recurrent inflammatory disease caused by the destruction of the intestinal mucosal epithelium that affects a growing number of people worldwide. Although the etiology of IBD is complex and still elucidated, the role of dysbiosis and dysregulated proteolysis is well recognized. Various studies observed altered composition and diversity of gut microbiota, as well as increased proteolytic activity (PA) in serum, plasma, colonic mucosa, and fecal supernatant of IBD compared to healthy individuals. The imbalance of intestinal microecology and intestinal protein hydrolysis were gradually considered to be closely related to IBD. Notably, the pivotal role of intestinal microbiota in maintaining proteolytic balance received increasing attention. In summary, we have speculated a mesmerizing story, regarding the hidden role of PA and microbiota-derived PA hidden in IBD. Most importantly, we provided the diagnosis and therapeutic targets for IBD as well as the formulation of new treatment strategies for other digestive diseases and protease-related diseases.
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Affiliation(s)
- Jun-Jie Hou
- Department of Gastroenterology, Shaoxing People's Hospital, Shaoxing, PR China
| | - Liang Ding
- Department of Gastroenterology, Shaoxing People's Hospital, Shaoxing, PR China
| | - Tao Yang
- Department of Gastroenterology, Shaoxing People's Hospital, Shaoxing, PR China
| | - Yan-Fei Yang
- Department of Gastroenterology, Shaoxing People's Hospital, Shaoxing, PR China
| | - Yue-Ping Jin
- Department of Gastroenterology, Shaoxing People's Hospital, Shaoxing, PR China
| | - Xiao-Ping Zhang
- Department of Gastroenterology, Shaoxing People's Hospital, Shaoxing, PR China
| | - A-Huo Ma
- Department of Gastroenterology, Shaoxing People's Hospital, Shaoxing, PR China
| | - Yue-Hua Qin
- Department of Gastroenterology, Shaoxing People's Hospital, Shaoxing, PR China.
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Cui M, Lee S, Ban SH, Ryu JR, Shen M, Yang SH, Kim JY, Choi SK, Han J, Kim Y, Han K, Lee D, Sun W, Kwon HB, Lee D. A single-component, light-assisted uncaging switch for endoproteolytic release. Nat Chem Biol 2024; 20:353-364. [PMID: 37973890 DOI: 10.1038/s41589-023-01480-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/12/2023] [Indexed: 11/19/2023]
Abstract
Proteases function as pivotal molecular switches, initiating numerous biological events. Notably, potyviral protease, derived from plant viruses, has emerged as a trusted proteolytic switch in synthetic biological circuits. To harness their capabilities, we have developed a single-component photocleavable switch, termed LAUNCHER (Light-Assisted UNcaging switCH for Endoproteolytic Release), by employing a circularly permutated tobacco etch virus protease and a blue-light-gated substrate, which are connected by fine-tuned intermodular linkers. As a single-component system, LAUNCHER exhibits a superior signal-to-noise ratio compared with multi-component systems, enabling precise and user-controllable release of payloads. This characteristic renders LAUNCHER highly suitable for diverse cellular applications, including transgene expression, tailored subcellular translocation and optochemogenetics. Additionally, the plug-and-play integration of LAUNCHER into existing synthetic circuits facilitates the enhancement of circuit performance. The demonstrated efficacy of LAUNCHER in improving existing circuitry underscores its significant potential for expanding its utilization in various applications.
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Affiliation(s)
- Mingguang Cui
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seunghwan Lee
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Sung Hwan Ban
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jae Ryun Ryu
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Meiying Shen
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Soo Hyun Yang
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jin Young Kim
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seul Ki Choi
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jaemin Han
- Korea University College of Medicine, Seoul, Republic of Korea
| | - Yoonhee Kim
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kihoon Han
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Donghun Lee
- Department of Physics, Korea University, Seoul, Republic of Korea
| | - Woong Sun
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hyung-Bae Kwon
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dongmin Lee
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea.
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea.
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43
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Daroodi Z, Taheri P. The genus Acrophialophora: History, phylogeny, morphology, beneficial effects and pathogenicity. Fungal Genet Biol 2024; 171:103875. [PMID: 38367800 DOI: 10.1016/j.fgb.2024.103875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 01/21/2024] [Accepted: 02/12/2024] [Indexed: 02/19/2024]
Abstract
The genus Acrophialophora is a thermotolerant fungus, which is widely distributed in temperate and tropical zones. This fungus is classified in Ascomycota and belongs to the Chaetomiaceae family and the genera of Parathielavia, Pseudothielavia and Hyalosphaerella are closely related to Acrophialophora. For this genus have been reported 28 species so far, which two species of Acrophialophora jodhpurensis and Acrophialophora teleoafricana produce only sexual phase and other species produce asexual form. Therefore, producing both sexual and asexual forms were not reported by any species. Many applications were reported by some species in agriculture, pharmacy and industry. Production of enzymes, antimicrobial metabolites and plant growth-promoting factors were reported by some species. The species of A. nainiana is used in the industries of textile, fruit juice, pulp and paper due to extracellular enzyme production. Also, other species produce extracellular enzymes that can be used in various industries. The species Acrophialophora are used in the composting industry due to the production of various enzymes and to be thermotolerant. In addition, some species were isolated from hostile environmental conditions. Therefore has been suggested that it can be used for mycoremediation. Also, antimicrobial metabolites of Acrophialophora have been reported to be effective against human and plant pathogens. In contrast to the beneficial effects described, the Acrophialophora pathogenicity has been rarely reported. Two species A. fusispora and A. levis are opportunistic fungi and have been reported as pathogens in humans, animals and plants. Currently, the development and applications of Acrophialophora species have increased more than past. To our knowledge, there is no report with comprehensive information on the species of Acrophialophora, which include their disadvantage and beneficial effects, particularly in agriculture. Therefore, it seems necessary to pay more in-depth attention to the application of this genus as a beneficial fungus in agriculture, pharmaceutical and industry. This review is focused on the history, phylogeny, morphology, valuable roles of Acrophialophora and pathogenicity.
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Affiliation(s)
- Zoha Daroodi
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Parissa Taheri
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
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44
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Mulero-Russe A, García AJ. Engineered Synthetic Matrices for Human Intestinal Organoid Culture and Therapeutic Delivery. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307678. [PMID: 37987171 PMCID: PMC10922691 DOI: 10.1002/adma.202307678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/02/2023] [Indexed: 11/22/2023]
Abstract
Human intestinal organoids (HIOs) derived from pluripotent stem cells or adult stem cell biopsies represent a powerful platform to study human development, drug testing, and disease modeling in vitro, and serve as a cell source for tissue regeneration and therapeutic advances in vivo. Synthetic hydrogels can be engineered to serve as analogs of the extracellular matrix to support HIO growth and differentiation. These hydrogels allow for tuning the mechanical and biochemical properties of the matrix, offering an advantage over biologically derived hydrogels such as Matrigel. Human intestinal organoids have been used for repopulating transplantable intestinal grafts and for in vivo delivery to an injured intestinal site. The use of synthetic hydrogels for in vitro culture and for in vivo delivery is expected to significantly increase the relevance of human intestinal organoids for drug screening, disease modeling, and therapeutic applications.
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Affiliation(s)
- Adriana Mulero-Russe
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Andrés J García
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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Naicker D, Rhoda C, Sunda F, Arowolo A. Unravelling the Intricate Roles of FAM111A and FAM111B: From Protease-Mediated Cellular Processes to Disease Implications. Int J Mol Sci 2024; 25:2845. [PMID: 38474092 DOI: 10.3390/ijms25052845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Proteases are critical enzymes in cellular processes which regulate intricate events like cellular proliferation, differentiation and apoptosis. This review highlights the multifaceted roles of the serine proteases FAM111A and FAM111B, exploring their impact on cellular functions and diseases. FAM111A is implicated in DNA replication and replication fork protection, thereby maintaining genome integrity. Additionally, FAM111A functions as an antiviral factor against DNA and RNA viruses. Apart from being involved in DNA repair, FAM111B, a paralog of FAM111A, participates in cell cycle regulation and apoptosis. It influences the apoptotic pathway by upregulating anti-apoptotic proteins and modulating cell cycle-related proteins. Furthermore, FAM111B's association with nucleoporins suggests its involvement in nucleo-cytoplasmic trafficking and plays a role in maintaining normal telomere length. FAM111A and FAM111B also exhibit some interconnectedness and functional similarity despite their distinct roles in cellular processes and associated diseases resulting from their dysfunction. FAM111A and FAM111B dysregulation are linked to genetic disorders: Kenny-Caffey Syndrome type 2 and Gracile Bone Dysplasia for FAM111A and POIKTMP, respectively, and cancers. Therefore, the dysregulation of these proteases in diseases emphasizes their potential as diagnostic markers and therapeutic targets. Future research is essential to unravel the intricate mechanisms governing FAM111A and FAM111B and explore their therapeutic implications comprehensively.
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Affiliation(s)
- Danielle Naicker
- Division of Medical Biochemistry, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Cenza Rhoda
- Hair and Skin Research Unit, Division of Dermatology, Department of Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Falone Sunda
- Hair and Skin Research Unit, Division of Dermatology, Department of Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Afolake Arowolo
- Hair and Skin Research Unit, Division of Dermatology, Department of Medicine, University of Cape Town, Cape Town 7925, South Africa
- Biomedical Research and Innovation Platform, South African Medical Research Council, Cape Town 7500, South Africa
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Hunt LC, Nyamkondiwa K, Stephan A, Jiao J, Kavdia K, Pagala V, Peng J, Demontis F. The ubiquitin-conjugating enzyme UBE2D/eff maintains a youthful proteome and ensures protein quality control during aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.12.571303. [PMID: 38168249 PMCID: PMC10759998 DOI: 10.1101/2023.12.12.571303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Ubiquitin-conjugating enzymes (E2s) are key for regulating protein function and turnover via ubiquitination but it remains undetermined which E2s maintain proteostasis during aging. Here, we find that E2s have diverse roles in handling a model aggregation-prone protein (huntingtin-polyQ) in the Drosophila retina: while some E2s mediate aggregate assembly, UBE2D/effete (eff) and other E2s are required for huntingtin-polyQ degradation. UBE2D/eff is key for proteostasis also in skeletal muscle: eff protein levels decline with aging, and muscle-specific eff knockdown causes an accelerated buildup in insoluble poly-ubiquitinated proteins (which progressively accumulate with aging) and shortens lifespan. Transgenic expression of human UBE2D2, homologous to eff, partially rescues the lifespan and proteostasis deficits caused by muscle-specific effRNAi by re-establishing the physiological levels of effRNAi-regulated proteins, which include several regulators of proteostasis. Interestingly, UBE2D/eff knockdown in young age reproduces part of the proteomic changes that normally occur in old muscles, suggesting that the decrease in UBE2D/eff protein levels that occurs with aging contributes to reshaping the composition of the muscle proteome. Altogether, these findings indicate that UBE2D/eff is a key E2 ubiquitin-conjugating enzyme that ensures protein quality control and helps maintain a youthful proteome composition during aging.
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Affiliation(s)
- Liam C. Hunt
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Kudzai Nyamkondiwa
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Anna Stephan
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jianqin Jiao
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Kanisha Kavdia
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Vishwajeeth Pagala
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Junmin Peng
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Fabio Demontis
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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47
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Borges PHO, Ferreira SB, Silva FP. Recent Advances on Targeting Proteases for Antiviral Development. Viruses 2024; 16:366. [PMID: 38543732 PMCID: PMC10976044 DOI: 10.3390/v16030366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 05/23/2024] Open
Abstract
Viral proteases are an important target for drug development, since they can modulate vital pathways in viral replication, maturation, assembly and cell entry. With the (re)appearance of several new viruses responsible for causing diseases in humans, like the West Nile virus (WNV) and the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), understanding the mechanisms behind blocking viral protease's function is pivotal for the development of new antiviral drugs and therapeutical strategies. Apart from directly inhibiting the target protease, usually by targeting its active site, several new pathways have been explored to impair its activity, such as inducing protein aggregation, targeting allosteric sites or by inducing protein degradation by cellular proteasomes, which can be extremely valuable when considering the emerging drug-resistant strains. In this review, we aim to discuss the recent advances on a broad range of viral proteases inhibitors, therapies and molecular approaches for protein inactivation or degradation, giving an insight on different possible strategies against this important class of antiviral target.
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Affiliation(s)
- Pedro Henrique Oliveira Borges
- Laboratory of Organic Synthesis and Biological Prospecting, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Sabrina Baptista Ferreira
- Laboratory of Organic Synthesis and Biological Prospecting, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
| | - Floriano Paes Silva
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
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48
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Mayr AL, Hummel K, Leitsch D, Razzazi-Fazeli E. A Comparison of Bottom-Up Proteomic Sample Preparation Methods for the Human Parasite Trichomonas vaginalis. ACS OMEGA 2024; 9:9782-9791. [PMID: 38434803 PMCID: PMC10905575 DOI: 10.1021/acsomega.3c10040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 03/05/2024]
Abstract
Bottom-up proteomic approaches depend on the efficient digestion of proteins into peptides for mass spectrometric analysis. Sample preparation strategies, based on magnetic beads, filter-aided systems, or in-solution digests, are commonly used for proteomic analysis. Time-intensive methods like filter-aided sample preparation (FASP) have led to the development of new, more time-efficient filter-based strategies like suspension trappings (S-Traps) or magnetic bead-based strategies like SP3. S-Traps have been reported as an alternative proteomic sample preparation method as they allow for high sodium dodecyl sulfate (SDS) concentrations to be present in the sample. In this study, we compare the efficiency of different protocols for FASP, SP3, and S-Trap-based digestion of proteins after extraction from Trichomonas vaginalis. Overall, we found a high number of protein IDs for all tested methods and a high degree of reproducibility within each method type. However, FASP with a 3 kDa cutoff filter unit outperformed the other methods analyzed, referring to the number of protein IDs. This is the first work providing the direct comparison of four different bottom-up proteomic approaches regarding the most efficient proteomic sample preparation protocol for the human parasite T. vaginalis.
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Affiliation(s)
- Anna-Lena Mayr
- VetCore
Facility, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - Karin Hummel
- VetCore
Facility, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - David Leitsch
- ISPTM, Medical
University of Vienna, Kinderspitalgasse 15, 1090 Vienna, Austria
| | - Ebrahim Razzazi-Fazeli
- VetCore
Facility, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
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Wang H, Zheng K, Wang M, Ma K, Ren L, Guo R, Ma L, Zhang H, Liu Y, Xiong Y, Wu M, Shao H, Sung YY, Mok WJ, Wong LL, McMinn A, Liang Y. Shewanella phage encoding a putative anti-CRISPR-like gene represents a novel potential viral family. Microbiol Spectr 2024; 12:e0336723. [PMID: 38214523 PMCID: PMC10846135 DOI: 10.1128/spectrum.03367-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 12/15/2023] [Indexed: 01/13/2024] Open
Abstract
Shewanella is a prevalent bacterial genus in deep-sea environments including marine sediments, exhibiting diverse metabolic capabilities that indicate its significant contributions to the marine biogeochemical cycles. However, only a few Shewanella phages were isolated and deposited in the NCBI database. In this study, we report the isolation and characterization of a novel Shewanella phage, vB_SbaS_Y11, that infects Shewanella KR11 and was isolated from the sewage in Qingdao, China. Transmission electron microscopy revealed that vB_SbaS_Y11 has an icosahedral head and a long tail. The genome of vB_SbaS_Y11 is a linear, double-stranded DNA with a length of 62,799 bp and a G+C content of 46.9%, encoding 71 putative open reading frames. No tRNA genes or integrase-related feature genes were identified. An uncharacterized anti-CRISPR AcrVA2 gene was detected in its genome. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analyses indicate that vB_SbaS_Y11 has a novel genomic architecture and shares low similarity to Pseudomonas virus H66 and Pseudomonas phage F116. vB_SbaS_Y11 represents a potential new family-level virus cluster with eight metagenomic assembled viral genomes named Ranviridae.IMPORTANCEThe Gram-negative Shewanella bacterial genus currently includes about 80 species of mostly aquatic Gammaproteobacteria, which were isolated around the globe in a multitude of environments, such as freshwater, seawater, coastal sediments, and the deepest trenches. Here, we present a Shewanella phage vB_SbaS_Y11 that contains an uncharacterized anti-CRISPR AcrVA2 gene and belongs to a potential virus family, Ranviridae. This study will enhance the knowledge about the genome, diversity, taxonomic classification, and global distribution of Shewanella phage populations.
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Affiliation(s)
- Hongmin Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Kaiyang Zheng
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Haide College, Ocean University of China, Qingdao, China
- Universiti Malaysia Terengganu-Ocean Unversity of China Joint Centre for Marine Studies, Qingdao, China
- The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Keran Ma
- Haide College, Ocean University of China, Qingdao, China
| | - Linyi Ren
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ruizhe Guo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Lina Ma
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hong Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yundan Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yao Xiong
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Miaolan Wu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Universiti Malaysia Terengganu-Ocean Unversity of China Joint Centre for Marine Studies, Qingdao, China
| | - Yeong Yik Sung
- Universiti Malaysia Terengganu-Ocean Unversity of China Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Wen Jye Mok
- Universiti Malaysia Terengganu-Ocean Unversity of China Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Li Lian Wong
- Universiti Malaysia Terengganu-Ocean Unversity of China Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Universiti Malaysia Terengganu-Ocean Unversity of China Joint Centre for Marine Studies, Qingdao, China
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50
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Ziegler AR, Dufour A, Scott NE, Edgington-Mitchell LE. Ion Mobility-Based Enrichment-Free N-Terminomics Analysis Reveals Novel Legumain Substrates in Murine Spleen. Mol Cell Proteomics 2024; 23:100714. [PMID: 38199506 PMCID: PMC10862022 DOI: 10.1016/j.mcpro.2024.100714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/19/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
Aberrant levels of the asparaginyl endopeptidase legumain have been linked to inflammation, neurodegeneration, and cancer, yet our understanding of this protease is incomplete. Systematic attempts to identify legumain substrates have been previously confined to in vitro studies, which fail to mirror physiological conditions and obscure biologically relevant cleavage events. Using high-field asymmetric waveform ion mobility spectrometry (FAIMS), we developed a streamlined approach for proteome and N-terminome analyses without the need for N-termini enrichment. Compared to unfractionated proteomic analysis, we demonstrate FAIMS fractionation improves N-termini identification by >2.5 fold, resulting in the identification of >2882 unique N-termini from limited sample amounts. In murine spleens, this approach identifies 6366 proteins and 2528 unique N-termini, with 235 cleavage events enriched in WT compared to legumain-deficient spleens. Among these, 119 neo-N-termini arose from asparaginyl endopeptidase activities, representing novel putative physiological legumain substrates. The direct cleavage of selected substrates by legumain was confirmed using in vitro assays, providing support for the existence of physiologically relevant extra-lysosomal legumain activity. Combined, these data shed critical light on the functions of legumain and demonstrate the utility of FAIMS as an accessible method to improve depth and quality of N-terminomics studies.
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Affiliation(s)
- Alexander R Ziegler
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Antoine Dufour
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada; McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Alberta, Canada
| | - Nichollas E Scott
- Department of Microbiology and Immunology, Peter Doherty Institute, The University of Melbourne, Parkville, Victoria, Australia.
| | - Laura E Edgington-Mitchell
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia.
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