1
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Costa GCA, Torquato RJS, de Morais Gomes V, Rosa-Fernandes L, Palmisano G, Tanaka AS. Functional characterization of a cystatin A from the bat Myotis davidii. Comp Biochem Physiol B Biochem Mol Biol 2024; 274:111003. [PMID: 38936799 DOI: 10.1016/j.cbpb.2024.111003] [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: 04/19/2024] [Revised: 06/06/2024] [Accepted: 06/23/2024] [Indexed: 06/29/2024]
Abstract
Myotis davidii cystatin A (MdCSTA), a stefin A-like from the Chinese native bat species M. davidii, was expressed as a recombinant protein and functionally characterized as a strong inhibitor of the cysteine proteases papain, human cathepsins L and B and the tick cathepsin L-like BmCL1. Despite the highly conserved amino acid sequences among stefins A from different vertebrates, MdCSTA presents a Methionine-2 residue at the N-terminal region and the second binding loop (pos 73-79) that differs from human stefin A (HsCSTA) and might be related to the lower inhibition constant (Ki) value presented by this inhibitor in comparison to human stefin A inhibition to cathepsin B. Therefore, to investigate the importance of these variable regions in cathepsin B inhibition, recombinant stefins A MdCSTA and HsCSTA containing mutations at the second amino acid residue and second binding loop were expressed and evaluated in kinetic assays. Enzymatic inhibition assays with cathepsin B revealed that switching the amino acid residues at position 2 and second binding loop region between bat and human CSTAs improved the HsCSTA's and reduced MdCSTA's inhibitory activity. Additionally, molecular docking analysis estimated lower energy values for the complex between MdCSTA-cathepsin B, in comparison to human CSTA-cathepsin B, while the mutants presented intermediate values, suggesting that other regions might contribute to the higher inhibitory activity against cathepsin B by MdCSTA. In conclusion, MdCSTA, the first bat's stefin A-like inhibitor to be functionally characterized, presented a higher inhibitory activity against cathepsin B in comparison to the human inhibitor, which is partially related to the glutamine-rich second binding loop and Met-2. Further structural analysis should be performed to elucidate potential inhibitor effects on cysteine proteinases.
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Affiliation(s)
| | | | - Vinícius de Morais Gomes
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, SP, Brazil
| | - Lívia Rosa-Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, SP, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, SP, Brazil
| | - Aparecida Sadae Tanaka
- Department of Biochemistry, Federal University of Sao Paulo (UNIFESP), SP, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), RJ, Brazil.
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2
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Radisky ES. Extracellular proteolysis in cancer: Proteases, substrates, and mechanisms in tumor progression and metastasis. J Biol Chem 2024; 300:107347. [PMID: 38718867 PMCID: PMC11170211 DOI: 10.1016/j.jbc.2024.107347] [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: 02/09/2024] [Revised: 04/08/2024] [Accepted: 04/25/2024] [Indexed: 06/02/2024] Open
Abstract
A vast ensemble of extracellular proteins influences the development and progression of cancer, shaped and reshaped by a complex network of extracellular proteases. These proteases, belonging to the distinct classes of metalloproteases, serine proteases, cysteine proteases, and aspartic proteases, play a critical role in cancer. They often become dysregulated in cancer, with increases in pathological protease activity frequently driven by the loss of normal latency controls, diminished regulation by endogenous protease inhibitors, and changes in localization. Dysregulated proteases accelerate tumor progression and metastasis by degrading protein barriers within the extracellular matrix (ECM), stimulating tumor growth, reactivating dormant tumor cells, facilitating tumor cell escape from immune surveillance, and shifting stromal cells toward cancer-promoting behaviors through the precise proteolysis of specific substrates to alter their functions. These crucial substrates include ECM proteins and proteoglycans, soluble proteins secreted by tumor and stromal cells, and extracellular domains of cell surface proteins, including membrane receptors and adhesion proteins. The complexity of the extracellular protease web presents a significant challenge to untangle. Nevertheless, technological strides in proteomics, chemical biology, and the development of new probes and reagents are enabling progress and advancing our understanding of the pivotal importance of extracellular proteolysis in cancer.
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Affiliation(s)
- Evette S Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, USA.
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3
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Peled A, Sprecher E. Proteolytic and Antiproteolytic Activity in the Skin: Gluing the Pieces Together. J Invest Dermatol 2024; 144:466-473. [PMID: 37865898 DOI: 10.1016/j.jid.2023.08.010] [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: 08/06/2023] [Accepted: 08/22/2023] [Indexed: 10/23/2023]
Abstract
Epidermal differentiation is ultimately aimed at the formation of a functional barrier capable of protecting the organism from the environment while preventing loss of biologically vital elements. Epidermal differentiation entails a delicately regulated process of cell-cell junction formation and dissolution to enable upward cell migration and desquamation. Over the past two decades, the deciphering of the genetic basis of a number of inherited conditions has delineated the pivotal role played in this process by a series of proteases and protease inhibitors, including serpins, cathepsins, and cystatins, suggesting novel avenues for therapeutic intervention in both rare and common disorders of cornification.
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Affiliation(s)
- Alon Peled
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Eli Sprecher
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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4
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Rangra S, Chakraborty R, Hasija Y, Aggarwal KK. A cystatin C similar protein from Musa acuminata that inhibits cathepsin B involved in rheumatoid arthritis using in silico approach and in vitro cathepsin B inhibition by protein extract. J Biomol Struct Dyn 2023; 41:10985-10998. [PMID: 37097972 DOI: 10.1080/07391102.2023.2203234] [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: 09/01/2022] [Accepted: 12/10/2022] [Indexed: 04/26/2023]
Abstract
Rheumatoid arthritis (RA) is an auto-immune disease that affects the synovial lining of the joints, causes synovitis and culminates to joint destruction. Cathepsin B is responsible for digesting unwanted proteins in extracellular matrix but its hyper expression could implicate in pathological diseases like RA. Available treatments for RA are classified into non-steroidal anti-inflammatory drugs (NSAIDs), disease-modifying anti-rheumatic drugs (DMARDs), and steroids, but the severe side effects associated with these drugs is one of concerns and cannot be ignored. Thus, any alternative therapy with minimum or no side effects would be a cornerstone. In our in silico studies a cystatin C similar protein (CCSP) has been identified from Musa acuminata that could effectively inhibit the cathepsin B activity. In silico and molecular dynamics studies showed that the identified CCSP and cathepsin B complex has binding energy -66.89 kcal/mol as compared to cystatin C - cathepsin B complex with binding energy of -23.38 kcal/mol. These results indicate that CCSP from Musa acuminata has better affinity towards cathepsin B as compared to its natural inhibitor cystatin C. Hence, CCSP may be suggested as an alternative therapeutic in combating RA by inhibiting its one of the key proteases cathepsin B. Further, in vitro experiments with fractionated protein extracts from Musa sp. peel inhibited cathepsin B to 98.30% at 300 µg protein concentration and its IC50 was found to be 45.92 µg indicating the presence of cathepsin B inhibitor(s) in protein extract of peel which was further confirmed by reverse zymography.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sabita Rangra
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | | | - Yasha Hasija
- Department of Biotechnology, Delhi Technological University, New Delhi, India
| | - Kamal Krishan Aggarwal
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
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5
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Martins LA, Buša M, Chlastáková A, Kotál J, Beránková Z, Stergiou N, Jmel MA, Schmitt E, Chmelař J, Mareš M, Kotsyfakis M. Protease-bound structure of Ricistatin provides insights into the mechanism of action of tick salivary cystatins in the vertebrate host. Cell Mol Life Sci 2023; 80:339. [PMID: 37898573 PMCID: PMC11071917 DOI: 10.1007/s00018-023-04993-4] [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: 05/12/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/30/2023]
Abstract
Tick saliva injected into the vertebrate host contains bioactive anti-proteolytic proteins from the cystatin family; however, the molecular basis of their unusual biochemical and physiological properties, distinct from those of host homologs, is unknown. Here, we present Ricistatin, a novel secreted cystatin identified in the salivary gland transcriptome of Ixodes ricinus ticks. Recombinant Ricistatin inhibited host-derived cysteine cathepsins and preferentially targeted endopeptidases, while having only limited impact on proteolysis driven by exopeptidases. Determination of the crystal structure of Ricistatin in complex with a cysteine cathepsin together with characterization of structural determinants in the Ricistatin binding site explained its restricted specificity. Furthermore, Ricistatin was potently immunosuppressive and anti-inflammatory, reducing levels of pro-inflammatory cytokines IL-6, IL-1β, and TNF-α and nitric oxide in macrophages; IL-2 and IL-9 levels in Th9 cells; and OVA antigen-induced CD4+ T cell proliferation and neutrophil migration. This work highlights the immunotherapeutic potential of Ricistatin and, for the first time, provides structural insights into the unique narrow selectivity of tick salivary cystatins determining their bioactivity.
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Affiliation(s)
- Larissa A Martins
- Institute of Parasitology, Branišovská 1160/31, 37005, Ceske Budejovice, Czech Republic
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, 59840, USA
| | - Michal Buša
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo N. 2, 16610, Prague, Czech Republic
| | - Adéla Chlastáková
- Department of Medical Biology, Faculty of Science, the University of South Bohemia in České Budějovice, Branišovská 1760C, 37005, Ceske Budejovice, Czech Republic
| | - Jan Kotál
- Institute of Parasitology, Branišovská 1160/31, 37005, Ceske Budejovice, Czech Republic
- Department of Medical Biology, Faculty of Science, the University of South Bohemia in České Budějovice, Branišovská 1760C, 37005, Ceske Budejovice, Czech Republic
| | - Zuzana Beránková
- Department of Medical Biology, Faculty of Science, the University of South Bohemia in České Budějovice, Branišovská 1760C, 37005, Ceske Budejovice, Czech Republic
| | - Natascha Stergiou
- Institute for Immunology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Mohamed Amine Jmel
- Institute of Parasitology, Branišovská 1160/31, 37005, Ceske Budejovice, Czech Republic
| | - Edgar Schmitt
- Institute for Immunology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Jindřich Chmelař
- Department of Medical Biology, Faculty of Science, the University of South Bohemia in České Budějovice, Branišovská 1760C, 37005, Ceske Budejovice, Czech Republic
| | - Michael Mareš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo N. 2, 16610, Prague, Czech Republic.
| | - Michail Kotsyfakis
- Institute of Parasitology, Branišovská 1160/31, 37005, Ceske Budejovice, Czech Republic.
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, N. Plastira 100, 70013, Heraklion, Crete, Greece.
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6
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Stoka V, Vasiljeva O, Nakanishi H, Turk V. The Role of Cysteine Protease Cathepsins B, H, C, and X/Z in Neurodegenerative Diseases and Cancer. Int J Mol Sci 2023; 24:15613. [PMID: 37958596 PMCID: PMC10650516 DOI: 10.3390/ijms242115613] [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: 07/22/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023] Open
Abstract
Papain-like cysteine proteases are composed of 11 human cysteine cathepsins, originally located in the lysosomes. They exhibit broad specificity and act as endopeptidases and/or exopeptidases. Among them, only cathepsins B, H, C, and X/Z exhibit exopeptidase activity. Recently, cysteine cathepsins have been found to be present outside the lysosomes and often participate in various pathological processes. Hence, they have been considered key signalling molecules. Their potentially hazardous proteolytic activities are tightly regulated. This review aims to discuss recent advances in understanding the structural aspects of these four cathepsins, mechanisms of their zymogen activation, regulation of their activities, and functional aspects of these enzymes in neurodegeneration and cancer. Neurodegenerative effects have been evaluated, particularly in Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, multiple sclerosis, and neuropsychiatric disorders. Cysteine cathepsins also participate in tumour progression and metastasis through the overexpression and secretion of proteases, which trigger extracellular matrix degradation. To our knowledge, this is the first review to provide an in-depth analysis regarding the roles of cysteine cathepsins B, H, C, and X in neurodegenerative diseases and cancer. Further advances in understanding the functions of cysteine cathepsins in these conditions will result in the development of novel, targeted therapeutic strategies.
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Affiliation(s)
- Veronika Stoka
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia;
- Jožef Stefan International Postgraduate School, SI-1000 Ljubljana, Slovenia
| | - Olga Vasiljeva
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia;
- CytomX Therapeutics, Inc., South San Francisco, CA 94080, USA
| | - Hiroshi Nakanishi
- Department of Pharmacology, Faculty of Pharmacy, Yasuda Women’s University, Hiroshima 731-0153, Japan;
| | - Vito Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia;
- Jožef Stefan International Postgraduate School, SI-1000 Ljubljana, Slovenia
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7
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Chakraborty S, Biswas S. Structure-Based Optimization of Protease-Inhibitor Interactions to Enhance Specificity of Human Stefin-A against Falcipain-2 from the Plasmodium falciparum 3D7 Strain. Biochemistry 2023; 62:1053-1069. [PMID: 36763907 DOI: 10.1021/acs.biochem.2c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The emergence of resistance in Plasmodium falciparum to frontline artemisinin-based combination therapies has raised global concerns and emphasized the identification of new drug targets for malaria. Cysteine protease falcipain-2 (FP2), involved in host hemoglobin degradation and instrumental in parasite survival, has long been proposed as a promising malarial drug target. However, designing active-site-targeted small-molecule inhibitors of FP2 becomes challenging due to their off-target specificity toward highly homologous human cysteine cathepsins. The use of proteinaceous inhibitors, which have nonconserved exosite interactions and larger interface area, can effectively circumvent this problem. In this study, we report for the first time that human stefin-A (STFA) efficiently inhibits FP2 with Ki values in the nanomolar range. The FP2-STFA complex crystal structure, determined in this study, and sequence analyses identify a unique nonconserved exosite interaction, compared to human cathepsins. Designing a mutation Lys68 > Arg in STFA amplifies its selectivity garnering a 3.3-fold lower Ki value against FP2, and the crystal structure of the FP2-STFAK68R complex shows stronger electrostatic interaction between side-chains of Arg68 (STFAK68R) and Asp109 (FP2). Comparative structural analyses and molecular dynamics (MD) simulation studies of the complexes further confirm higher buried surface areas, better interaction energies for FP2-STFAK68R, and consistency of the newly developed electrostatic interaction (STFA-R68-FP2-D109) in the MD trajectory. The STFA-K68R mutant also shows higher Ki values against human cathepsin-L and stefin, a step toward eliminating off-target specificity. Hence, this work underlines the design of host-based proteinaceous inhibitors against FP2, with further optimization to render them more potent and selective.
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Affiliation(s)
- Subhoja Chakraborty
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, 1/AF Bidhan Nagar, Kolkata 700064, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Sampa Biswas
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, 1/AF Bidhan Nagar, Kolkata 700064, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
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8
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Zamyatnin AA, Gregory LC, Townsend PA, Soond SM. Beyond basic research: the contribution of cathepsin B to cancer development, diagnosis and therapy. Expert Opin Ther Targets 2022; 26:963-977. [PMID: 36562407 DOI: 10.1080/14728222.2022.2161888] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION In view of other candidate proteins from the cathepsin family of proteases holding great potential in being targeted during cancer therapy, the importance of Cathepsin B (CtsB) stands out as being truly exceptional. Based on its contribution to oncogenesis, its intimate connection with regulating apoptosis and modulating extracellular and intracellular functions through its secretion or compartmentalized subcellular localization, collectively highlight its complex molecular involvement with a myriad of normal and pathological regulatory processes. Despite its complex functional nature, CtsB is emerging as one of the few cathepsin proteases that has been extensively researched to yield tangible outcomes for cancer therapy. AREAS COVERED In this article, we review the scientific literature that has justified or shaped the importance of CtsB expression in cancer progression, from the perspective of highlighting a paradigm that is rapidly changing from basic research toward a broader clinical and translational context. EXPERT OPINION In doing so, we detail its maturation as a diagnostic marker through describing the development of CtsB-specific Activity-Based Probes, the rapid evolution of these toward a new generation of Prodrugs, and the evaluation of these in model systems for their therapeutic potential as anti-cancer agents in the clinic.
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Affiliation(s)
- Andrey A Zamyatnin
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russian Federation.,Department of Biotechnology, Sirius University of Science and Technology, Sochi, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Levy C Gregory
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Paul A Townsend
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Surinder M Soond
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russian Federation
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9
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Rudzinska-Radecka M, Frolova AS, Balakireva AV, Gorokhovets NV, Pokrovsky VS, Sokolova DV, Korolev DO, Potoldykova NV, Vinarov AZ, Parodi A, Zamyatnin AA. In Silico, In Vitro, and Clinical Investigations of Cathepsin B and Stefin A mRNA Expression and a Correlation Analysis in Kidney Cancer. Cells 2022; 11:1455. [PMID: 35563761 PMCID: PMC9101197 DOI: 10.3390/cells11091455] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 02/06/2023] Open
Abstract
The cysteine protease Cathepsin B (CtsB) plays a critical role in multiple signaling pathways, intracellular protein degradation, and processing. Endogenous inhibitors regulate its enzymatic activity, including stefins and other cystatins. Recent data proved that CtsB is implicated in tumor extracellular matrix remodeling, cell invasion, and metastasis: a misbalance between cathepsins and their natural inhibitors is often considered a sign of disease progression. In the present study, we investigated CtsB and stefin A (StfA) expression in renal cell carcinoma (RCC). mRNA analysis unveiled a significant CTSB and STFA increase in RCC tissues compared to adjacent non-cancerogenic tissues and a higher CtsB expression in malignant tumors than in benign renal neoplasms. Further analysis highlighted a positive correlation between CtsB and StfA expression as a function of patient sex, age, tumor size, grade, lymph node invasion, metastasis occurrence, and survival. Alternative overexpression and silencing of CtsB and StfA confirmed the correlation expression between these proteins in human RCC-derived cells through protein analysis and fluorescent microscopy. Finally, the ectopic expression of CtsB and StfA increased RCC cell proliferation. Our data strongly indicated that CtsB and StfA expression play an important role in RCC development by mutually stimulating their expression in RCC progression.
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Affiliation(s)
- Magdalena Rudzinska-Radecka
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (M.R.-R.); (A.S.F.); (A.V.B.); (N.V.G.); (A.P.)
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Anastasia S. Frolova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (M.R.-R.); (A.S.F.); (A.V.B.); (N.V.G.); (A.P.)
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave., 354340 Sochi, Russia; (V.S.P.); (D.V.S.)
| | - Anastasia V. Balakireva
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (M.R.-R.); (A.S.F.); (A.V.B.); (N.V.G.); (A.P.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Neonila V. Gorokhovets
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (M.R.-R.); (A.S.F.); (A.V.B.); (N.V.G.); (A.P.)
| | - Vadim S. Pokrovsky
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave., 354340 Sochi, Russia; (V.S.P.); (D.V.S.)
- Laboratory of Combined Treatment, N.N. Blokhin Cancer Research Center, 115478 Moscow, Russia
- Department of Biochemistry, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Darina V. Sokolova
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave., 354340 Sochi, Russia; (V.S.P.); (D.V.S.)
- Laboratory of Combined Treatment, N.N. Blokhin Cancer Research Center, 115478 Moscow, Russia
- Department of Biochemistry, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Dmitry O. Korolev
- Institute for Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.O.K.); (N.V.P.); (A.Z.V.)
| | - Natalia V. Potoldykova
- Institute for Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.O.K.); (N.V.P.); (A.Z.V.)
| | - Andrey Z. Vinarov
- Institute for Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.O.K.); (N.V.P.); (A.Z.V.)
| | - Alessandro Parodi
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (M.R.-R.); (A.S.F.); (A.V.B.); (N.V.G.); (A.P.)
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave., 354340 Sochi, Russia; (V.S.P.); (D.V.S.)
| | - Andrey A. Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (M.R.-R.); (A.S.F.); (A.V.B.); (N.V.G.); (A.P.)
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave., 354340 Sochi, Russia; (V.S.P.); (D.V.S.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Department of Immunology, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
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10
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Zhong H, Chen Z, Lin J, Xu Y, Liu D, Yin X. The inhibition mechanism of carp (
Cyprinus carpio
) stefin to cathepsin B and their tertiary structures. Int J Food Sci Technol 2021. [DOI: 10.1111/ijfs.15265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Haixia Zhong
- Department of Agricultural Technology Neijiang Vocational and Technical College Neijiang 641100 China
| | - Zhiguang Chen
- Department of Agricultural Technology Neijiang Vocational and Technical College Neijiang 641100 China
| | - Jianhe Lin
- Department of Agricultural Technology Neijiang Vocational and Technical College Neijiang 641100 China
| | - Yi Xu
- Department of Agricultural Technology Neijiang Vocational and Technical College Neijiang 641100 China
| | - Dan Liu
- Department of Agricultural Technology Neijiang Vocational and Technical College Neijiang 641100 China
| | - Xianfeng Yin
- Department of Agricultural Technology Neijiang Vocational and Technical College Neijiang 641100 China
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11
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Yasui N, Nakamura K, Yamashita A. A sweet protein monellin as a non-antibody scaffold for synthetic binding proteins. J Biochem 2021; 169:585-599. [PMID: 33386843 DOI: 10.1093/jb/mvaa147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/07/2020] [Indexed: 11/13/2022] Open
Abstract
Synthetic binding proteins that have the ability to bind with molecules can be generated using various protein domains as non-antibody scaffolds. These designer proteins have been used widely in research studies, as their properties overcome the disadvantages of using antibodies. Here, we describe the first application of a phage display to generate synthetic binding proteins using a sweet protein, monellin, as a non-antibody scaffold. Single-chain monellin (scMonellin), in which two polypeptide chains of natural monellin are connected by a short linker, has two loops on one side of the molecule. We constructed phage display libraries of scMonellin, in which the amino acid sequence of the two loops is diversified. To validate the performance of these libraries, we sorted them against the folding mutant of the green fluorescent protein variant (GFPuv) and yeast small ubiquitin-related modifier. We successfully obtained scMonellin variants exhibiting moderate but significant affinities for these target proteins. Crystal structures of one of the GFPuv-binding variants in complex with GFPuv revealed that the two diversified loops were involved in target recognition. scMonellin, therefore, represents a promising non-antibody scaffold in the design and generation of synthetic binding proteins. We termed the scMonellin-derived synthetic binding proteins 'SWEEPins'.
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Affiliation(s)
- Norihisa Yasui
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Kazuaki Nakamura
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Atsuko Yamashita
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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12
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Wang Y, Wang L, Li X, Qu X, Han N, Ruan M, Zhang C. Decreased CSTA expression promotes lymphatic metastasis and predicts poor survival in oral squamous cell carcinoma. Arch Oral Biol 2021; 126:105116. [PMID: 33831734 DOI: 10.1016/j.archoralbio.2021.105116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/21/2021] [Accepted: 03/29/2021] [Indexed: 01/10/2023]
Abstract
OBJECTIVE Herein, we aimed to identify biomarkers that affect lymphatic metastasis of oral squamous cell carcinoma (OSCC) through bioinformatic analysis, and clinicopathological and in vitro verifications. DESIGN The OSCC-related gene expression dataset was retrieved from The Cancer Genome Atlas (TCGA) and analyzed to identify differentially expressed genes (DEGs), which were subjected to pathway analysis. Weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) network analysis were performed to identify hub genes. Expression of potential biomarkers was examined using quantitative real-time polymerase chain reaction, immunohistochemistry, and western blotting. Statistical analyses were performed to determine the association between biomarker expression and clinicopathological characteristics of patients with OSCC. Effects of selected biomarkers on proliferation, migration, and invasion were evaluated using in vitro assays. RESULTS For DEGs, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed potential lymphatic metastasis-related biological processes and signaling pathways. Eight hub genes - ALOXE3, CSTA, PLA2G4E, PPL, SPRR1A, SPRR2A, SPRR2D, and SPRR2E, were identified via WGCNA and PPI analyses. CSTA expression was markedly downregulated in primary OSCC tissues, and low CSTA expression significantly correlated with high tumor grade (P = 0.001), nodal metastasis (P = 0.028), and poor overall survival (P < 0.001). CTSA overexpression inhibited OSCC cell migration and invasion in vitro, with little effect on OSCC cell proliferation. CONCLUSIONS Our study revealed that CSTA is a promising biomarker and therapeutic target with prognostic implications in patients with OSCC. CSTA may play an essential role in OSCC lymphatic metastasis and tumor differentiation.
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Affiliation(s)
- Yupu Wang
- Department of Oral & Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China; National Center for Stomatology, Shanghai, 200011, China; National Clinical Research Center for Oral Diseases, Shanghai, 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
| | - Lin Wang
- Department of Oral & Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China; National Center for Stomatology, Shanghai, 200011, China; National Clinical Research Center for Oral Diseases, Shanghai, 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
| | - Xing Li
- Department of Oral & Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China; National Center for Stomatology, Shanghai, 200011, China; National Clinical Research Center for Oral Diseases, Shanghai, 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China; School of Stomatology, Weifang Medical University, Weifang, 261031, Shandong, China
| | - Xingzhou Qu
- Department of Oral & Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China; National Center for Stomatology, Shanghai, 200011, China; National Clinical Research Center for Oral Diseases, Shanghai, 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
| | - Nannan Han
- Department of Oral & Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China; National Center for Stomatology, Shanghai, 200011, China; National Clinical Research Center for Oral Diseases, Shanghai, 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China.
| | - Min Ruan
- Department of Oral & Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China; National Center for Stomatology, Shanghai, 200011, China; National Clinical Research Center for Oral Diseases, Shanghai, 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China.
| | - Chenping Zhang
- Department of Oral & Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China; National Center for Stomatology, Shanghai, 200011, China; National Clinical Research Center for Oral Diseases, Shanghai, 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
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13
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Tušar L, Usenik A, Turk B, Turk D. Mechanisms Applied by Protein Inhibitors to Inhibit Cysteine Proteases. Int J Mol Sci 2021; 22:997. [PMID: 33498210 PMCID: PMC7863939 DOI: 10.3390/ijms22030997] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/13/2021] [Accepted: 01/16/2021] [Indexed: 02/07/2023] Open
Abstract
Protein inhibitors of proteases are an important tool of nature to regulate and control proteolysis in living organisms under physiological and pathological conditions. In this review, we analyzed the mechanisms of inhibition of cysteine proteases on the basis of structural information and compiled kinetic data. The gathered structural data indicate that the protein fold is not a major obstacle for the evolution of a protease inhibitor. It appears that nature can convert almost any starting fold into an inhibitor of a protease. In addition, there appears to be no general rule governing the inhibitory mechanism. The structural data make it clear that the "lock and key" mechanism is a historical concept with limited validity. However, the analysis suggests that the shape of the active site cleft of proteases imposes some restraints. When the S1 binding site is shaped as a pocket buried in the structure of protease, inhibitors can apply substrate-like binding mechanisms. In contrast, when the S1 binding site is in part exposed to solvent, the substrate-like inhibition cannot be employed. It appears that all proteases, with the exception of papain-like proteases, belong to the first group of proteases. Finally, we show a number of examples and provide hints on how to engineer protein inhibitors.
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Affiliation(s)
- Livija Tušar
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; (L.T.); (A.U.); (B.T.)
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Aleksandra Usenik
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; (L.T.); (A.U.); (B.T.)
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; (L.T.); (A.U.); (B.T.)
- Faculty of Chemistry, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
- Institute of Regenerative Medicine, I.M. Sechenov First Moscow State Medical University, Bol’shaya Pirogovskaya Ulitsa, 19c1, 119146 Moscow, Russia
| | - Dušan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; (L.T.); (A.U.); (B.T.)
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
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14
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Shibao PYT, Santos-Júnior CD, Santiago AC, Mohan C, Miguel MC, Toyama D, Vieira MAS, Narayanan S, Figueira A, Carmona AK, Schiermeyer A, Soares-Costa A, Henrique-Silva F. Sugarcane cystatins: From discovery to biotechnological applications. Int J Biol Macromol 2020; 167:676-686. [PMID: 33285201 DOI: 10.1016/j.ijbiomac.2020.11.185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/01/2022]
Abstract
Phytocystatins are tight-binding cysteine protease inhibitors produced by plants. The first phytocystatin described was isolated from Oryza sativa and, since then, cystatins from several plant species were reported, including from sugarcane. Sugarcane cystatins were unraveled in Sugarcane EST project database, after sequencing of cDNA libraries from various sugarcane tissues at different developmental stages and six sugarcane cystatins were cloned, expressed and characterized (CaneCPI-1 to CaneCPI-6). These recombinant proteins were produced in different expression systems and inhibited several cysteine proteases, including human cathepsins B and L, which can be involved in pathologies, such as cancer. In this review, we summarize a comprehensive history of all sugarcane cystatins, presenting an updated phylogenetic analysis; chromosomal localization, and genomic organization. We also present protein docking of CaneCPI-5 in the active site of human cathepsin B, insights about canecystatins structures; recombinant expression in different systems, comparison of their inhibitory activities against human cysteine cathepsins B, K, L, S, V, falcipains from Plasmodium falciparum and a cathepsin L-like from the sugarcane weevil Sphenophorus levis; and enlighten their potential and current applications in agriculture and health.
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Affiliation(s)
- Priscila Yumi Tanaka Shibao
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil; Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Aachen, Germany
| | - Célio Dias Santos-Júnior
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, China
| | | | - Chakravarthi Mohan
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Mariana Cardoso Miguel
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Danyelle Toyama
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | | | - Subramonian Narayanan
- Genetic Transformation Laboratory, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Antonio Figueira
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Adriana K Carmona
- Department of Biophysics, Federal University of São Paulo, Escola Paulista de Medicina, São Paulo, Brazil
| | - Andreas Schiermeyer
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Aachen, Germany
| | - Andrea Soares-Costa
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Flavio Henrique-Silva
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil.
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15
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Dolenc I, Štefe I, Turk D, Taler-Verčič A, Turk B, Turk V, Stoka V. Human cathepsin X/Z is a biologically active homodimer. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140567. [PMID: 33227497 DOI: 10.1016/j.bbapap.2020.140567] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 12/15/2022]
Abstract
Human cathepsin X belongs to the cathepsin family of 11 lysosomal cysteine proteases. We expressed recombinant procathepsin X in Pichia pastoris in vitro and cleaved it into its active mature form using aspartic cathepsin E. We found, using size exclusion chromatography, X-ray crystallography, and small-angle X-ray scattering, that cathepsin X is a biologically active homodimer with a molecular weight of ~53 kDa. The novel finding that cathepsin X is a dimeric protein opens new horizons in the understanding of its function and the underlying pathophysiological mechanisms of various diseases including neurodegenerative disorders in humans.
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Affiliation(s)
- Iztok Dolenc
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
| | - Ivica Štefe
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Dušan Turk
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia; Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Ajda Taler-Verčič
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Vito Turk
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova 39, SI-1000 Ljubljana, Slovenia.
| | - Veronika Stoka
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
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16
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Tabish TA, Pranjol MZI, Whatmore JL, Zhang S. Status and Future Directions of Anti-metastatic Cancer Nanomedicines for the Inhibition of Cathepsin L. FRONTIERS IN NANOTECHNOLOGY 2020. [DOI: 10.3389/fnano.2020.00001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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17
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Hook V, Yoon M, Mosier C, Ito G, Podvin S, Head BP, Rissman R, O'Donoghue AJ, Hook G. Cathepsin B in neurodegeneration of Alzheimer's disease, traumatic brain injury, and related brain disorders. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140428. [PMID: 32305689 DOI: 10.1016/j.bbapap.2020.140428] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/31/2020] [Accepted: 04/08/2020] [Indexed: 12/21/2022]
Abstract
Investigations of Alzheimer's disease (AD), traumatic brain injury (TBI), and related brain disorders have provided extensive evidence for involvement of cathepsin B, a lysosomal cysteine protease, in mediating the behavioral deficits and neuropathology of these neurodegenerative diseases. This review integrates findings of cathepsin B regulation in clinical biomarker studies, animal model genetic and inhibitor evaluations, structural studies, and lysosomal cell biological mechanisms in AD, TBI, and related brain disorders. The results together indicate the role of cathepsin B in the behavioral deficits and neuropathology of these disorders. Lysosomal leakage occurs in AD and TBI, and related neurodegeneration, which leads to the hypothesis that cathepsin B is redistributed from the lysosome to the cytosol where it initiates cell death and inflammation processes associated with neurodegeneration. These results together implicate cathepsin B as a major contributor to these neuropathological changes and behavioral deficits. These findings support the investigation of cathepsin B as a potential drug target for therapeutic discovery and treatment of AD, TBI, and TBI-related brain disorders.
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Affiliation(s)
- Vivian Hook
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States of America; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, United States of America; Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, United States of America.
| | - Michael Yoon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States of America; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, United States of America
| | - Charles Mosier
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States of America
| | - Gen Ito
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States of America
| | - Sonia Podvin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States of America
| | - Brian P Head
- VA San Diego Healthcare System, La Jolla, CA, United States of America; Department of Anesthesia, University of California San Diego, La Jolla, CA, United States of America
| | - Robert Rissman
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, United States of America; VA San Diego Healthcare System, La Jolla, CA, United States of America
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States of America
| | - Gregory Hook
- American Life Sciences Pharmaceuticals, Inc., La Jolla, CA, United States of America
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18
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Dai Z, Cheng Q, Zhang Y. Rational Design of a Humanized Antibody Inhibitor of Cathepsin B. Biochemistry 2020; 59:1420-1427. [PMID: 32212642 DOI: 10.1021/acs.biochem.0c00046] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cathepsin B (CTSB) is an abundant cysteine protease that functions in both endolysosomal compartments and extracellular regions. A considerable number of preclinical and clinical studies indicate that CTSB is implicated in many human diseases. Expression levels and activity of CTSB significantly correlate with disease progression and severity. Current inhibitors of CTSB are lack of adequate specificity and pharmacological activities. Through structure-guided rational design, we hereby designed and generated a humanized antibody inhibitor targeting human CTSB. This was achieved by genetically fusing the propeptide of procathepsin B, a naturally occurring inhibitor of CTSB, into heavy chain complementarity-determining region 3 (CDR3H) of Herceptin that is used in the clinic for the treatment of breast cancer. The resulting antibody-propeptide fusion displayed high specificity for inhibiting CTSB proteolytic activity at nanomolar levels. Pharmacokinetic studies in mice revealed a plasma half-life of approximately 42 h for this anti-CTSB antibody inhibitor, comparable to that of the parental Herceptin scaffold. This study demonstrates a new approach for the efficient generation of humanized antibody inhibitors with high potency and specificity for human CTSB, which may be extended to develop antibody inhibitors against other disease relevant cathepsin proteases.
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Affiliation(s)
- Zhefu Dai
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
| | - Qinqin Cheng
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
| | - Yong Zhang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States.,Department of Chemistry, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California 90089, United States.,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089, United States.,Research Center for Liver Diseases, University of Southern California, Los Angeles, California 90089, United States
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19
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Soond SM, Kozhevnikova MV, Townsend PA, Zamyatnin AA. Cysteine Cathepsin Protease Inhibition: An update on its Diagnostic, Prognostic and Therapeutic Potential in Cancer. Pharmaceuticals (Basel) 2019; 12:ph12020087. [PMID: 31212661 PMCID: PMC6630828 DOI: 10.3390/ph12020087] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/06/2019] [Accepted: 06/08/2019] [Indexed: 12/22/2022] Open
Abstract
In keeping with recent developments in basic research; the importance of the Cathepsins as targets in cancer therapy have taken on increasing importance and given rise to a number of key areas of interest in the clinical setting. In keeping with driving basic research in this area in a translational direction; recent findings have given rise to a number of exciting developments in the areas of cancer diagnosis; prognosis and therapeutic development. As a fast-moving area of research; the focus of this review brings together the latest findings and highlights the translational significance of these developments.
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Affiliation(s)
- Surinder M Soond
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Trubetskaya str. 8-2, 119991 Moscow, Russia.
| | - Maria V Kozhevnikova
- Federal State Autonomous Edu-cational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Healthcare of the Russian Federation (Sechenovskiy University), Hospital Therapy Department No. 1, 6-1 Bolshaya Pirogovskaya str, 119991 Moscow, Russia.
| | - Paul A Townsend
- Division of Cancer Sciences and Manchester Cancer Research Centre, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, and the NIHR Manchester Biomedical Research Centre, Manchester M20 4GJ, UK.
| | - Andrey A Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Trubetskaya str. 8-2, 119991 Moscow, Russia.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia.
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20
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Bratovš A, Kramer L, Mikhaylov G, Vasiljeva O, Turk B. Stefin A-functionalized liposomes as a system for cathepsins S and L-targeted drug delivery. Biochimie 2019; 166:94-102. [PMID: 31163196 DOI: 10.1016/j.biochi.2019.05.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 05/30/2019] [Indexed: 01/26/2023]
Abstract
Proteolytic activity in the tumor microenvironment is one of the key elements supporting tumor development and metastasis. One of the key families of proteases that are overexpressed in various types of cancer and implicated in different stages of tumor progression are cysteine cathepsins. Among them, cathepsins S and L can be secreted into the tumor microenvironment by tumor and/or immune cells, making them promising drug delivery targets. Here we present a new system for cathepsin S/L targeting using a liposomal drug carrier system functionalized with the endogenous cysteine cathepsin inhibitor, stefin A. The selective targeting of cathepsins by stefin A-conjugated liposomes was confirmed in vitro and in vivo, demonstrating the potential of this approach for cancer diagnosis and treatment.
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Affiliation(s)
- Andreja Bratovš
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia; Jozef Stefan International Postgraduate School, Jamova 39, Sl-1000 Ljubljana, Slovenia
| | - Lovro Kramer
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Georgy Mikhaylov
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Olga Vasiljeva
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, Večna Pot 113, University of Ljubljana, SI-1000 Ljubljana, Slovenia.
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21
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Liu J, Svärd SG, Klotz C. Giardia intestinalis cystatin is a potent inhibitor of papain, parasite cysteine proteases and, to a lesser extent, human cathepsin B. FEBS Lett 2019; 593:1313-1325. [PMID: 31077354 DOI: 10.1002/1873-3468.13433] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/16/2019] [Accepted: 05/04/2019] [Indexed: 11/09/2022]
Abstract
Cystatins are important regulators of papain-like cysteine proteases. In the protozoan parasite Giardia intestinalis, papain-like cysteine proteases play an essential role in the parasite's biology and pathogenicity. Here, we characterized a cysteine protease inhibitor of G. intestinalis that belongs to type-I-cystatins. The parasite cystatin is shown to be a strong inhibitor of papain (Ki ≈ 0.3 nm) and three parasite cysteine proteases (CP14019, CP16160 and CP16779, Ki ≈ 0.9-5.8 nm), but a weaker inhibitor of human cathepsin B (Ki ≈ 79.9 nm). The protein localizes mainly in the cytoplasm. Together, these data suggest that cystatin of G. intestinalis plays a role in the regulation of cysteine protease activities in the parasite and, possibly, in the interaction with the host.
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Affiliation(s)
- Jingyi Liu
- Department of Cell and Molecular Biology, BMC, Uppsala University, Sweden
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, BMC, Uppsala University, Sweden
| | - Christian Klotz
- Department of Mycotic and Parasitic Agents and Mycobacteria (FG16), Robert Koch-Institute, Berlin, Germany
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22
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Cystatins in cancer progression: More than just cathepsin inhibitors. Biochimie 2019; 166:233-250. [PMID: 31071357 DOI: 10.1016/j.biochi.2019.05.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/03/2019] [Indexed: 12/20/2022]
Abstract
Cystatins are endogenous and reversible inhibitors of cysteine peptidases that are important players in cancer progression. Besides their primary role as regulators of cysteine peptidase activity, cystatins are involved in cancer development and progression through proteolysis-independent mechanisms. Mechanistic studies of cystatin function revealed that they affect all stages of cancer progression including tumor growth, apoptosis, invasion, metastasis and angiogenesis. Recently, the involvement of cystatins in the antitumor immune responses was reported. In this review, we discuss molecular mechanisms and clinical aspects of cystatins in cancer. Altered expression of cystatins in cancer resulting in harmful excessive cysteine peptidase activity has been a subject of several studies in order to find correlations with clinical outcome and therapy response. However, involvement in anti-tumor immune response and signaling cascades leading to cancer progression designates cystatins as possible targets for development of new anti-tumor drugs.
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23
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Wang Y, Niu H, Hu Z, Zhu M, Wang L, Han L, Qian L, Tian K, Yuan H, Lou H. Targeting the lysosome by an aminomethylated Riccardin D triggers DNA damage through cathepsin B-mediated degradation of BRCA1. J Cell Mol Med 2018; 23:1798-1812. [PMID: 30565390 PMCID: PMC6378192 DOI: 10.1111/jcmm.14077] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 12/21/2022] Open
Abstract
RD-N, an aminomethylated derivative of riccardin D, is a lysosomotropic agent that can trigger lysosomal membrane permeabilization followed by cathepsin B (CTSB)-dependent apoptosis in prostate cancer (PCa) cells, but the underlying mechanisms remain unknown. Here we show that RD-N treatment drives CTSB translocation from the lysosomes to the nucleus where it promotes DNA damage by suppression of the breast cancer 1 protein (BRCA1). Inhibition of CTSB activity with its specific inhibitors, or by CTSB-targeting siRNA or CTSB with enzyme-negative domain attenuated activation of BRCA1 and DNA damage induced by RD-N. Conversely, CTSB overexpression resulted in inhibition of BRCA1 and sensitized PCa cells to RD-N-induced cell death. Furthermore, RD-N-induced cell death was exacerbated in BRCA1-deficient cancer cells. We also demonstrated that CTSB/BRCA1-dependent DNA damage was critical for RD-N, but not for etoposide, reinforcing the importance of CTSB/BRCA1 in RD-N-mediated cell death. In addition, RD-N synergistically increased cell sensitivity to cisplatin, and this effect was more evidenced in BRCA1-deficient cancer cells. This study reveals a novel molecular mechanism that RD-N promotes CTSB-dependent DNA damage by the suppression of BRCA1 in PCa cells, leading to the identification of a potential compound that target lysosomes for cancer treatment.
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Affiliation(s)
- Yanyan Wang
- Key Lab of Chemical Biology of Ministry of Education, Department of Natural Product Chemistry, School of Pharmaceutical sciences, Shandong University, Jinan, China
| | - Huanmin Niu
- Institute of Medical Science, The Second Hospital of Shandong University, Jinan, China
| | - Zhongyi Hu
- Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, China
| | - Mengyuan Zhu
- Key Lab of Chemical Biology of Ministry of Education, Department of Natural Product Chemistry, School of Pharmaceutical sciences, Shandong University, Jinan, China
| | - Lining Wang
- Key Lab of Chemical Biology of Ministry of Education, Department of Natural Product Chemistry, School of Pharmaceutical sciences, Shandong University, Jinan, China
| | - Lili Han
- School of Medicine, Shandong Yingcai University, Jinan, China
| | - Lilin Qian
- Institute of Medical Science, The Second Hospital of Shandong University, Jinan, China
| | - Keli Tian
- Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, China
| | - Huiqing Yuan
- Institute of Medical Science, The Second Hospital of Shandong University, Jinan, China
| | - Hongxiang Lou
- Key Lab of Chemical Biology of Ministry of Education, Department of Natural Product Chemistry, School of Pharmaceutical sciences, Shandong University, Jinan, China
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24
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Manconi B, Liori B, Cabras T, Vincenzoni F, Iavarone F, Castagnola M, Messana I, Olianas A. Salivary Cystatins: Exploring New Post-Translational Modifications and Polymorphisms by Top-Down High-Resolution Mass Spectrometry. J Proteome Res 2018; 16:4196-4207. [PMID: 29019242 DOI: 10.1021/acs.jproteome.7b00567] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Cystatins are a complex family of cysteine peptidase inhibitors. In the present study, various proteoforms of cystatin A, cystatin B, cystatin S, cystatin SN, and cystatin SA were detected in the acid-soluble fraction of human saliva and characterized by a top-down HPLC-ESI-MS approach. Proteoforms of cystatin D were also detected and characterized by an integrated top-down and bottom-up strategy. The proteoforms derive from coding sequence polymorphisms and post-translational modifications, in particular, phosphorylation, N-terminal processing, and oxidation. This study increases the current knowledge of salivary cystatin proteoforms and provides the basis to evaluate possible qualitative/quantitative variations of these proteoforms in different pathological states and reveal new potential salivary biomarkers of disease. Data are available via ProteomeXchange with identifier PXD007170.
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Affiliation(s)
- Barbara Manconi
- Department of Life and Environmental Sciences, Biomedical Section, University of Cagliari , Monserrato Campus, 09042 Monserrato, Cagliari, Italy
| | - Barbara Liori
- Department of Life and Environmental Sciences, Biomedical Section, University of Cagliari , Monserrato Campus, 09042 Monserrato, Cagliari, Italy
| | - Tiziana Cabras
- Department of Life and Environmental Sciences, Biomedical Section, University of Cagliari , Monserrato Campus, 09042 Monserrato, Cagliari, Italy
| | - Federica Vincenzoni
- Biochemistry and Clinical Biochemistry Institute, Medicine Faculty, Catholic University of Rome , L.go F. Vito 1, 00168 Rome, Italy
| | - Federica Iavarone
- Biochemistry and Clinical Biochemistry Institute, Medicine Faculty, Catholic University of Rome , L.go F. Vito 1, 00168 Rome, Italy
| | - Massimo Castagnola
- Biochemistry and Clinical Biochemistry Institute, Medicine Faculty, Catholic University of Rome , L.go F. Vito 1, 00168 Rome, Italy.,Institute of Chemistry of the Molecular Recognition CNR , L.go F. Vito 1, 00168 Rome, Italy
| | - Irene Messana
- Biochemistry and Clinical Biochemistry Institute, Medicine Faculty, Catholic University of Rome , L.go F. Vito 1, 00168 Rome, Italy.,Institute of Chemistry of the Molecular Recognition CNR , L.go F. Vito 1, 00168 Rome, Italy
| | - Alessandra Olianas
- Department of Life and Environmental Sciences, Biomedical Section, University of Cagliari , Monserrato Campus, 09042 Monserrato, Cagliari, Italy
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25
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Onming S, Thongda W, Li C, Sawatdichaikul O, McMillan N, Klinbunga S, Peatman E, Poompuang S. Bioinformatics characterization of a cathepsin B transcript from the giant river prawn, Macrobrachium rosenbergii: Homology modeling and expression analysis after Aeromonas hydrophila infection. Comp Biochem Physiol B Biochem Mol Biol 2018; 221-222:18-28. [PMID: 29649577 DOI: 10.1016/j.cbpb.2018.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Cathepsin B is a lysosomal proteolytic enzyme that has been suggested to play a role in pathological processes of immune system. In this study, the full-length cDNA sequence of cathepsin B transcript in the giant river prawn Macrobrachium rosenbergii (MrCTSB) was obtained from 454 pyrosequencing of cDNAs from hepatopancreas and muscle. It was 1158 bp in length, containing an open reading frame (ORF) of 987 bp corresponding to 328 amino acids. The predicted molecular mass and pI of MrCTSB protein was 36.04 kDa and 4.73. The major characteristics of MrCTSB protein consisted of a propeptide of C1 peptidase family at the N-terminus and a cysteine protease (Pept_C1) domain at the C-terminus. The 3-dimentional structure of MrCTSB was constructed by computer-assisted homology modeling. The folding of MrCTSB was highly conserved to human CTSB structure and the modeled MrCTSB displayed characteristics of cysteine proteinases superfamily. The docking study was performed to investigate binding interactions between known inhibitors against MrCTSB. Known inhibitors were oriented in the groove of catalytic site cleft. They bound to subsites from S2, S1, S1', and S2', respectively, with key residues in each subsite. Challenge of juvenile prawns with Aeromonas hydrophila revealed that the MrCTSB transcript in hepatopancreas significantly increased at 60-96 h post injection (hpi). This suggested that MrCTSB may play roles in innate immunity of M. rosenbergii. Our results provide useful information for a more comprehensive study in immune-related functions of MrCTSB.
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Affiliation(s)
- Saowalak Onming
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan Road, Bangkok 10900, Thailand
| | - Wilawan Thongda
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Chao Li
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao 266109, China
| | - Orathai Sawatdichaikul
- Department of Nutrition and Health, Institute of Food Research and Product Development, Kasetsart University, Bangkok 10900, Thailand
| | - Nichanun McMillan
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan Road, Bangkok 10900, Thailand
| | - Sirawut Klinbunga
- Aquatic Molecular Genetics and Biotechnology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Paholyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; Center of Excellence for Marine Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Eric Peatman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Supawadee Poompuang
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan Road, Bangkok 10900, Thailand.
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26
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Anzai R, Asami Y, Inoue W, Ueno H, Yamada K, Okada T. Evaluation of variability in high-resolution protein structures by global distance scoring. Heliyon 2018; 4:e00510. [PMID: 29560428 PMCID: PMC5857612 DOI: 10.1016/j.heliyon.2018.e00510] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/12/2017] [Accepted: 01/08/2018] [Indexed: 01/22/2023] Open
Abstract
Systematic analysis of the statistical and dynamical properties of proteins is critical to understanding cellular events. Extraction of biologically relevant information from a set of high-resolution structures is important because it can provide mechanistic details behind the functional properties of protein families, enabling rational comparison between families. Most of the current structural comparisons are pairwise-based, which hampers the global analysis of increasing contents in the Protein Data Bank. Additionally, pairing of protein structures introduces uncertainty with respect to reproducibility because it frequently accompanies other settings for superimposition. This study introduces intramolecular distance scoring for the global analysis of proteins, for each of which at least several high-resolution structures are available. As a pilot study, we have tested 300 human proteins and showed that the method is comprehensively used to overview advances in each protein and protein family at the atomic level. This method, together with the interpretation of the model calculations, provide new criteria for understanding specific structural variation in a protein, enabling global comparison of the variability in proteins from different species.
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Affiliation(s)
| | | | | | | | | | - Tetsuji Okada
- Department of Life Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
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27
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Caracelli I, Maganhi SH, de Oliveira Cardoso J, Cunha RL, Vega-Teijido MA, Zukerman-Schpector J, Tiekink ER. Crystallographic and docking (Cathepsins B, K, L and S) studies on bioactive halotelluroxetanes. Z KRIST-CRYST MATER 2017. [DOI: 10.1515/zkri-2017-2079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The molecular structures of the halotelluroxetanes p-MeOC6H4Te(X)[C(=C(H)X′)C(CH2)nO], X=X′=Cl and n=6 (1) and X=Cl, X′=Br and n=5 (4), show similar binuclear aggregates sustained by {· · ·Te–O}2 cores comprising covalent Te–O and secondary Te· · ·O interactions. The resulting C2ClO2(lone-pair) sets define pseudo-octahedral geometries. In each structure, C–X· · ·π(arene) interactions lead to supramolecular layers. Literature studies have shown these and related compounds (i.e. 2: X=X′=Cl and n=5; 3: X=X′=Br and n=5) to inhibit Cathepsins B, K, L and S to varying extents. Molecular docking calculations have been conducted on ligands (i.e. cations derived by removal of the tellurium-bound X atoms) 1′–3′ (note 3′=4′) enabling correlations between affinity for sub-sites and inhibition. The common feature of all docked complexes was the formation of a Te–S covalent bond with cysteine residues, the relative stability of the ligands with an E-configuration and the formation of a C–O· · ·π interaction with the phenyl ring; for 1′ the Te–S covalent bond was weak, a result correlating with its low inhibition profile. At the next level differences are apparent, especially with respect to the interactions formed by the organic-ligand-bound halides. While these atoms do not form specific interactions in Cathepsins B and K, in Cathepsin L, these halides are involved in C–O· · ·X halogen bonds.
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Affiliation(s)
- Ignez Caracelli
- BioMat, Departamento de Física , Universidade Federal de São Carlos , C.P. 676 , São Carlos, SP, 13565-905 , Brazil
| | - Stella H. Maganhi
- BioMat, Programa de Pós-graduação em Biotecnologia , Universidade Federal de São Carlos , C.P. 676 , São Carlos, SP, 13565-905 , Brazil
| | - Josiane de Oliveira Cardoso
- BioMat, Departamento de Física , Universidade Federal de São Carlos , C.P. 676 , São Carlos, SP, 13565-905 , Brazil
| | - Rodrigo L.O.R. Cunha
- Center of Natural Sciences and Humanities, Federal University of ABC , Santo André, São Paulo 09210-180 , Brazil
| | - Mauricio Angel Vega-Teijido
- Laboratório de Cristalografia, Estereodinâmica e Modelagem Molecular , Departamento de Química , Universidade Federal de São Carlos , C.P. 676 , São Carlos, SP, 13565-905 , Brazil
| | - Julio Zukerman-Schpector
- Laboratório de Cristalografia, Estereodinâmica e Modelagem Molecular , Departamento de Química , Universidade Federal de São Carlos , C.P. 676 , São Carlos, SP, 13565-905 , Brazil
| | - Edward R.T. Tiekink
- Research Centre for Crystalline Materials, School of Science and Technology , Sunway University , 47500 Bandar Sunway , Selangor Darul Ehsan , Malaysia
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28
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Monteiro Júnior JE, Valadares NF, Pereira HD, Dyszy FH, da Costa Filho AJ, Uchôa AF, de Oliveira AS, da Silveira Carvalho CP, Grangeiro TB. Expression in Escherichia coli of cysteine protease inhibitors from cowpea (Vigna unguiculata): The crystal structure of a single-domain cystatin gives insights on its thermal and pH stability. Int J Biol Macromol 2017; 102:29-41. [DOI: 10.1016/j.ijbiomac.2017.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/26/2017] [Accepted: 04/03/2017] [Indexed: 10/19/2022]
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29
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Malhotra P, Udgaonkar JB. Secondary Structural Change Can Occur Diffusely and Not Modularly during Protein Folding and Unfolding Reactions. J Am Chem Soc 2016; 138:5866-78. [DOI: 10.1021/jacs.6b03356] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pooja Malhotra
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jayant B. Udgaonkar
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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30
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Chalcones, semicarbazones and pyrazolines as inhibitors of cathepsins B, H and L. Int J Biol Macromol 2015; 80:710-24. [PMID: 26193682 PMCID: PMC7124378 DOI: 10.1016/j.ijbiomac.2015.07.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 07/13/2015] [Accepted: 07/15/2015] [Indexed: 11/22/2022]
Abstract
Three bio macromolecules cathepsins B, H and L of physiological and pathological significance have been selected for the study. The molecules have been designed by combining two important pharmacophores their cyclized analogues and were studied for their inhibitory effects on selected enzymes. Two isomeric forms of chalconesemicarbazones are reported for the first time. The synthesized compounds showed a competitive inhibition towards cathepsins B, H and L. Docking experiments were run along with to relate with in vitro studies.
Cathepsin B [EC 3.4.22.1], cathepsin H [EC 3.4.22.16] and cathepsin L [EC 3.4.22.15] are the most versatile lysosomal cysteine proteases and are responsible for intracellular protein degradation. These are involved in a number of pathological conditions including tissue degenerative processes. In the present work, we report the synthesis and systematic evaluation of differently substituted chalcones, chalconesemicarbazones, and diarylpyrazolines on cathepsins B, H and L activity. It was found that after a preliminary screening as cysteine protease inhibitors, chalconesemicarbazones were better inhibitors to these cysteine proteases than diarylpyrazolines followed by chalcones. All the synthesized compounds were identified as the best inhibitors to cathepsin L followed by cathepsin B and then cathepsin H. The results are compared with docking studies and it was found that all the compounds resulted in decrease in energy while interacting with the active site of the enzyme.
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31
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Yadav VK, Mandal RS, Puniya BL, Singh S, Yadav S. Studies on the interactions of SAP-1 (an N-terminal truncated form of cystatin S) with its binding partners by CD-spectroscopic and molecular docking methods. J Biomol Struct Dyn 2015; 33:147-57. [PMID: 24261636 DOI: 10.1080/07391102.2013.855882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SAP-1 is a 113 amino acid long single-chain protein which belongs to the type 2 cystatin gene family. In our previous study, we have purified SAP-1 from human seminal plasma and observed its cross-class inhibitory property. At this time, we report the interaction of SAP-1 with diverse proteases and its binding partners by CD-spectroscopic and molecular docking methods. The circular dichroism (CD) spectroscopic studies demonstrate that the conformation of SAP-1 is changed after its complexation with proteases, and the alterations in protein secondary structure are quantitatively calculated with increase of α-helices and reduction of β-strand content. To get insight into the interactions between SAP-1 and proteases, we make an effort to model the three-dimensional structure of SAP-1 by molecular modeling and verify its stability and viability through molecular dynamics simulations and finally complexed with different proteases using ClusPro 2.0 Server. A high degree of shape complementarity is examined within the complexes, stabilized by a number of hydrogen bonds (HBs) and hydrophobic interactions. Using HB analyses in different protein complexes, we have identified a series of key residues that may be involved in the interactions between SAP-1 and proteases. These findings will assist to understand the mechanism of inhibition of SAP-1 for different proteases and provide intimation for further research.
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Affiliation(s)
- Vikash Kumar Yadav
- a Department of Biophysics , All India Institute of Medical Sciences , Delhi 110029 , India
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32
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Mashamba-Thompson T, Soliman MES. Insight into the binding theme of CA-074Me to cathepsin B: molecular dynamics simulations and scaffold hopping to identify potential analogues as anti-neurodegenerative diseases. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1145-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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33
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Theoretical insight into the mechanism for the inhibition of the cysteine protease cathepsin B by 1,2,4-thiadiazole derivatives. J Mol Model 2014; 20:2254. [DOI: 10.1007/s00894-014-2254-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 04/21/2014] [Indexed: 10/25/2022]
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34
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Shankar R, Samykutty A, Riggin C, Kannan S, Wenzel U, Kolhatkar R. Cathepsin B degradable star-shaped peptidic macromolecules for delivery of 2-methoxyestradiol. Mol Pharm 2013; 10:3776-88. [PMID: 23971990 DOI: 10.1021/mp400261h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
2-Methoxyestradiol (2ME), a natural metabolite of estradiol, has antiproliferative and antiangiogenic activity. However, its clinical success is limited due to poor water solubility and poor pharmacokinetic parameters suggesting the need for a delivery vehicle. In this study we evaluated cathepsin B degradable star-shaped peptidic macromolecules (SPMs) that can potentially be used to create higher generation and high molecular weight peptidic polymer as delivery vehicle of 2ME. Two peptidic macromolecules having positively charged amine (ASPM) or negatively charged carboxyl surface groups (CSPM) were synthesized and evaluated for their degradation in the presence of cathepsin B and stability in the presence of neutral or acidic buffer and serum. Both ASPM and CSPM degraded rapidly in the presence of cathepsin B. Both were stable in neutral and acidic buffer whereas only CSPM exhibited substantial stability in the presence of serum. Both macromolecules were nontoxic toward breast cancer cells whereas 2ME-containing macromolecules exhibited antiproliferative activity in the micromolar range. Overall, results from the current study indicate that tetrapeptide GFLG can be used to create star-shaped macromolecules that are degraded in the presence of cathepsin B and have the potential to be developed as delivery vehicles of 2ME.
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Affiliation(s)
- Ravi Shankar
- Department of Biopharmaceutical Sciences, University of Illinois Chicago , Rockford, Illinois 61107, United States
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35
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Valadares NF, Oliveira‐Silva R, Cavini IA, Almeida Marques I, D'Muniz Pereira H, Soares‐Costa A, Henrique‐Silva F, Kalbitzer HR, Munte CE, Garratt RC. X
‐ray crystallography and
NMR
studies of domain‐swapped canecystatin‐1. FEBS J 2013; 280:1028-38. [DOI: 10.1111/febs.12095] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Revised: 11/29/2012] [Accepted: 12/03/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Napoleão F. Valadares
- Center for Structural Molecular Biotechnology Department of Physics and Informatics Physics Institute of São Carlos University of São Paulo São Carlos‐SP Brazil
| | - Rodrigo Oliveira‐Silva
- Center for Structural Molecular Biotechnology Department of Physics and Informatics Physics Institute of São Carlos University of São Paulo São Carlos‐SP Brazil
| | - Italo A. Cavini
- Center for Structural Molecular Biotechnology Department of Physics and Informatics Physics Institute of São Carlos University of São Paulo São Carlos‐SP Brazil
| | | | - Humberto D'Muniz Pereira
- Center for Structural Molecular Biotechnology Department of Physics and Informatics Physics Institute of São Carlos University of São Paulo São Carlos‐SP Brazil
| | - Andrea Soares‐Costa
- Laboratory of Molecular Biology Department of Genetic and Evolution Federal University of São Carlos Brazil
| | - Flavio Henrique‐Silva
- Laboratory of Molecular Biology Department of Genetic and Evolution Federal University of São Carlos Brazil
| | - Hans R. Kalbitzer
- Institute of Biophysics and Physical Biochemistry University of Regensburg Germany
| | - Claudia E. Munte
- Center for Structural Molecular Biotechnology Department of Physics and Informatics Physics Institute of São Carlos University of São Paulo São Carlos‐SP Brazil
| | - Richard C. Garratt
- Center for Structural Molecular Biotechnology Department of Physics and Informatics Physics Institute of São Carlos University of São Paulo São Carlos‐SP Brazil
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36
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Sosič I, Mirković B, Arenz K, Stefane B, Kos J, Gobec S. Development of new cathepsin B inhibitors: combining bioisosteric replacements and structure-based design to explore the structure-activity relationships of nitroxoline derivatives. J Med Chem 2013; 56:521-33. [PMID: 23252745 DOI: 10.1021/jm301544x] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human cathepsin B has many house-keeping functions, such as protein turnover in lysosomes. However, dysregulation of its activity is associated with numerous diseases, including cancers. We present here the structure-based design and synthesis of new cathepsin B inhibitors using the cocrystal structure of 5-nitro-8-hydroxyquinoline in the cathepsin B active site. A focused library of over 50 compounds was prepared by modifying positions 5, 7, and 8 of the parent compound nitroxoline. The kinetic parameters and modes of inhibition were characterized, and the selectivities of the most promising inhibitors were determined. The best performing inhibitor 17 was effective in cell-based in vitro models of tumor invasion, where it significantly abrogated invasion of MCF-10A neoT cells. These data show that we have successfully explored the structure-activity relationships of nitroxoline derivatives to provide new inhibitors that could eventually lead to compounds with clinical usefulness against the deleterious effects of cathepsin B in cancer progression.
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Affiliation(s)
- Izidor Sosič
- University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
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37
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Siricoon S, Grams SV, Grams R. Efficient inhibition of cathepsin B by a secreted type 1 cystatin of Fasciola gigantica. Mol Biochem Parasitol 2012; 186:126-33. [DOI: 10.1016/j.molbiopara.2012.10.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 10/09/2012] [Accepted: 10/10/2012] [Indexed: 12/14/2022]
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38
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Solution structure of a phytocystatin from Ananas comosus and its molecular interaction with papain. PLoS One 2012; 7:e47865. [PMID: 23139757 PMCID: PMC3490968 DOI: 10.1371/journal.pone.0047865] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 09/24/2012] [Indexed: 11/19/2022] Open
Abstract
The structure of a recombinant pineapple cystatin (AcCYS) was determined by NMR with the RMSD of backbone and heavy atoms of twenty lowest energy structures of 0.56 and 1.11 Å, respectively. It reveals an unstructured N-terminal extension and a compact inhibitory domain comprising a four-stranded antiparallel β-sheet wrapped around a central α-helix. The three structural motifs (G(45), Q(89)XVXG, and W(120)) putatively responsible for the interaction with papain-like proteases are located in one side of AcCYS. Significant chemical shift perturbations in two loop regions, residues 45 to 48 (GIYD) and residues 89 to 91 (QVV), of AcCYS strongly suggest their involvement in the binding to papain, consistent with studies on other members of the cystatin family. However, the highly conserved W120 appears not to be involved in the binding with papain as no chemical shift perturbation was observed. Chemical shift index analysis further indicates that the length of the α-helix is shortened upon association with papain. Collectively, our data suggest that AcCYS undergoes local secondary structural rearrangements when papain is brought into close contact. A molecular model of AcCYS/papain complex is proposed to illustrate the interaction between AcCYS and papain, indicating a complete blockade of the catalytic triad by AcCYS.
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Martínez M, Cambra I, González-Melendi P, Santamaría ME, Díaz I. C1A cysteine-proteases and their inhibitors in plants. PHYSIOLOGIA PLANTARUM 2012; 145:85-94. [PMID: 22221156 DOI: 10.1111/j.1399-3054.2012.01569.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Plant cysteine-proteases (CysProt) represent a well-characterized type of proteolytic enzymes that fulfill tightly regulated physiological functions (senescence and seed germination among others) and defense roles. This article is focused on the group of papain-proteases C1A (family C1, clan CA) and their inhibitors, phytocystatins (PhyCys). In particular, the protease-inhibitor interaction and their mutual participation in specific pathways throughout the plant's life are reviewed. C1A CysProt and PhyCys have been molecularly characterized, and comparative sequence analyses have identified consensus functional motifs. A correlation can be established between the number of identified CysProt and PhyCys in angiosperms. Thus, evolutionary forces may have determined a control role of cystatins on both endogenous and pest-exogenous proteases in these species. Tagging the proteases and inhibitors with fluorescence proteins revealed common patterns of subcellular localization in the endoplasmic reticulum-Golgi network in transiently transformed onion epidermal cells. Further in vivo interactions were demonstrated by bimolecular fluorescent complementation, suggesting their participation in the same physiological processes.
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Affiliation(s)
- Manuel Martínez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Campus Montegancedo, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain
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40
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Abstract
Biochemical activity and core stability are essential properties of proteins, maintained usually by conserved amino acids. Structural dynamics emerged in recent years as another essential aspect of protein functionality. Structural dynamics enable the adaptation of the protein to binding substrates and to undergo allosteric transitions, while maintaining the native fold. Key residues that mediate structural dynamics would thus be expected to be conserved or exhibit coevolutionary patterns at least. Yet, the correlation between sequence evolution and structural dynamics is yet to be established. With recent advances in efficient characterization of structural dynamics, we are now in a position to perform a systematic analysis. In the present study, a set of 34 enzymes representing various folds and functional classes is analyzed using information theory and elastic network models. Our analysis shows that the structural regions distinguished by their coevolution propensity as well as high mobility are predisposed to serve as substrate recognition sites, whereas residues acting as global hinges during collective dynamics are often supported by conserved residues. We propose a mobility scale for different types of amino acids, which tends to vary inversely with amino acid conservation. Our findings suggest the balance between physical adaptability (enabled by structure-encoded motions) and chemical specificity (conferred by correlated amino acid substitutions) underlies the selection of a relatively small set of versatile folds by proteins.
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Affiliation(s)
- Ying Liu
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, USA
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41
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Cysteine cathepsins: from structure, function and regulation to new frontiers. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1824:68-88. [PMID: 22024571 PMCID: PMC7105208 DOI: 10.1016/j.bbapap.2011.10.002] [Citation(s) in RCA: 881] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/03/2011] [Accepted: 10/04/2011] [Indexed: 02/06/2023]
Abstract
It is more than 50 years since the lysosome was discovered. Since then its hydrolytic machinery, including proteases and other hydrolases, has been fairly well identified and characterized. Among these are the cysteine cathepsins, members of the family of papain-like cysteine proteases. They have unique reactive-site properties and an uneven tissue-specific expression pattern. In living organisms their activity is a delicate balance of expression, targeting, zymogen activation, inhibition by protein inhibitors and degradation. The specificity of their substrate binding sites, small-molecule inhibitor repertoire and crystal structures are providing new tools for research and development. Their unique reactive-site properties have made it possible to confine the targets simply by the use of appropriate reactive groups. The epoxysuccinyls still dominate the field, but now nitriles seem to be the most appropriate “warhead”. The view of cysteine cathepsins as lysosomal proteases is changing as there is now clear evidence of their localization in other cellular compartments. Besides being involved in protein turnover, they build an important part of the endosomal antigen presentation. Together with the growing number of non-endosomal roles of cysteine cathepsins is growing also the knowledge of their involvement in diseases such as cancer and rheumatoid arthritis, among others. Finally, cysteine cathepsins are important regulators and signaling molecules of an unimaginable number of biological processes. The current challenge is to identify their endogenous substrates, in order to gain an insight into the mechanisms of substrate degradation and processing. In this review, some of the remarkable advances that have taken place in the past decade are presented. This article is part of a Special Issue entitled: Proteolysis 50 years after the discovery of lysosome.
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42
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Blaydon DC, Nitoiu D, Eckl KM, Cabral RM, Bland P, Hausser I, van Heel DA, Rajpopat S, Fischer J, Oji V, Zvulunov A, Traupe H, Hennies HC, Kelsell DP. Mutations in CSTA, encoding Cystatin A, underlie exfoliative ichthyosis and reveal a role for this protease inhibitor in cell-cell adhesion. Am J Hum Genet 2011; 89:564-71. [PMID: 21944047 DOI: 10.1016/j.ajhg.2011.09.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 08/26/2011] [Accepted: 09/02/2011] [Indexed: 11/30/2022] Open
Abstract
Autosomal-recessive exfoliative ichthyosis presents shortly after birth as dry, scaly skin over most of the body with coarse peeling of nonerythematous skin on the palms and soles, which is exacerbated by excessive moisture and minor trauma. Using whole-genome homozygosity mapping, candidate-gene analysis and deep sequencing, we have identified loss-of-function mutations in the gene for protease inhibitor cystatin A (CSTA) as the underlying genetic cause of exfoliative ichthyosis. We found two homozygous mutations, a splice-site and a nonsense mutation, in two consanguineous families of Bedouin and Turkish origin. Electron microscopy of skin biopsies from affected individuals revealed that the level of detachment occurs in the basal and lower suprabasal layers. In addition, in vitro modeling suggests that in the absence of cystatin A protein, there is a cell-cell adhesion defect in human keratinocytes that is particularly prominent when cells are subject to mechanical stress. We show here evidence of a key role for a protease inhibitor in epidermal adhesion within the lower layers of the human epidermis.
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Affiliation(s)
- Diana C Blaydon
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, UK
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