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Zhou X, Chen H, Huang D, Guan G, Ma X, Cai W, Liao J, Guan T. Reduced expression of cathepsin F predicts poor prognosis in patients with clear cell renal cell carcinoma. Sci Rep 2024; 14:13556. [PMID: 38866930 PMCID: PMC11169360 DOI: 10.1038/s41598-024-64542-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 06/10/2024] [Indexed: 06/14/2024] Open
Abstract
Abnormalities in the extracellular matrix (ECM) play important roles in the regulation and progression of clear cell renal cell carcinoma (ccRCC). The cysteine cathepsin is one of the major proteases involved in ECM remodeling and has been shown to be aberrantly expressed in multiple cancer types. However, the clinical significance and biological function of distinct cysteine cathepsins in ccRCC remain poorly understood. In this study, several bioinformatics databases, including UALCAN, TIMER, GEPIA and the Human Protein Atlas datasets, were used to analyze the expression and prognostic value of different cysteine cathepsin family members in ccRCC. We found that the expression level of CTSF was downregulated in tumor tissues and closely related to the poor survival of ccRCC patients. Further in vitro experiments suggested that CTSF overexpression suppressed the proliferation and migration of ccRCC cells. Moreover, the expression of CTSF was shown to be associated with several immune-infiltrating cells and immunomodulators in ccRCC. These results indicated that CTSF might be a promising diagnostic and prognostic marker in ccRCC.
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Affiliation(s)
- Xin Zhou
- School of Chemistry and Environmental Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Huayan Chen
- Department of Pharmacy, Affiliated Hospital of Guangdong Medical University, Guangdong, 524001, China
| | - Dong Huang
- Department of Pharmacy, Affiliated Hospital of Guangdong Medical University, Guangdong, 524001, China
| | - Guixian Guan
- Department of Gastroenterology, Heyuan People's Hospital, Heyuan, China
| | - Xiaoli Ma
- Department of Pharmacy, Affiliated Hospital of Guangdong Medical University, Guangdong, 524001, China
| | - Weiming Cai
- Department of Pharmacy, Affiliated Hospital of Guangdong Medical University, Guangdong, 524001, China.
| | - Jing Liao
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guangdong Medical University, Guangdong, 524001, China.
| | - Tangming Guan
- Department of Pharmacy, Affiliated Hospital of Guangdong Medical University, Guangdong, 524001, China.
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Zdravkova K, Mijanovic O, Brankovic A, Ilicheva PM, Jakovleva A, Karanovic J, Pualic M, Pualic D, Rubel AA, Savvateeva LV, Parodi A, Zamyatnin AA. Unveiling the Roles of Cysteine Proteinases F and W: From Structure to Pathological Implications and Therapeutic Targets. Cells 2024; 13:917. [PMID: 38891048 PMCID: PMC11171618 DOI: 10.3390/cells13110917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024] Open
Abstract
Cysteine cathepsins F and W are members of the papain-like cysteine protease family, which have distinct structural features and functional roles in various physiological and pathological processes. This review provides a comprehensive overview of the current understanding of the structure, biological functions, and pathological implications of cathepsins F and W. Beginning with an introduction to these proteases, we delve into their structural characteristics and elucidate their unique features that dictate their enzymatic activities and substrate specificity. We also explore the intricate involvement of cathepsins F and W in malignancies, highlighting their role as potential biomarkers and therapeutic targets in cancer progression. Furthermore, we discuss the emerging roles of these enzymes in immune response modulation and neurological disorders, shedding light on their implications in autoimmune and neurodegenerative diseases. Finally, we review the landscape of inhibitors targeting these proteases, highlighting their therapeutic potential and challenges in clinical translation. This review brings together the diverse facets of cysteine cathepsins F and W, providing insights into their roles in health and disease and guiding future investigations for therapeutic advances.
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Affiliation(s)
- Kristina Zdravkova
- AD Alkaloid Skopje, Boulevard Alexander the Great 12, 1000 Skopje, North Macedonia;
| | - Olja Mijanovic
- Dia-M, LCC, 7 b.3 Magadanskaya Str., 129345 Moscow, Russia;
| | - Ana Brankovic
- Department of Forensic Sciences, Faculty of Forensic Sciences and Engineering, University of Criminal Investigation and Police Studies, Cara Dusana 196, 11000 Belgrade, Serbia;
| | - Polina M. Ilicheva
- Institute of Chemistry, Saratov State University, Astrakhanskaya Street 83, 410012 Saratov, Russia;
| | | | - Jelena Karanovic
- Laboratory for Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444A, 11000 Belgrade, Serbia;
| | - Milena Pualic
- Institute Cardiovascular Diseases Dedinje, Heroja Milana Tepica 1, 11000 Belgrade, Serbia;
| | - Dusan Pualic
- Military Medical Academy, Crnotravska 17, 11000 Belgrade, Serbia;
| | - Aleksandr A. Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Lyudmila V. Savvateeva
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Alessandro Parodi
- Research Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia;
| | - Andrey A. Zamyatnin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
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Wang YL, Zhu MY, Yuan ZF, Ren XY, Guo XT, Hua Y, Xu L, Zhao CY, Jiang LH, Zhang X, Sheng GX, Jiang PF, Zhao ZY, Gao F. Proteomic profiling of cerebrospinal fluid in pediatric myelin oligodendrocyte glycoprotein antibody-associated disease. World J Pediatr 2024; 20:259-271. [PMID: 36507981 PMCID: PMC10957615 DOI: 10.1007/s12519-022-00661-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 11/15/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Myelin oligodendrocyte glycoprotein (MOG) antibody-associated disease (MOGAD) is an autoimmune demyelinating disorder of the central nervous system. METHODS Extracted proteins from 34 cerebrospinal fluid (CSF) samples [patients with MOGAD (MOG group, n = 12); healthy controls (HC group, n = 12); patients with MOG seronegative and metagenomics next-generation sequencing-negative inflammatory neurological diseases (IND group, n = 10)] were processed and subjected to label-free quantitative proteomics. Supervised partial least squares-discriminant analysis (PLS-DA) and orthogonal PLS-DA (O-PLS-DA) models were also performed based on proteomics data. Functional analysis of differentially expressed proteins (DEPs) was performed using Gene Ontology, InterPro, and Kyoto Encyclopedia Genes and Genomes. An enzyme-linked immunosorbent assay was used to determine the complement levels in serum from patients with MOGAD. RESULTS Four hundred and twenty-nine DEPs (149 upregulated and 280 downregulated proteins) were identified in the MOG group compared to the HC group according to the P value and fold change (FC). Using the O-PLS-DA model, 872 differentially abundant proteins were identified with variable importance projection (VIP) scores > 1. Five proteins (gamma-glutamyl hydrolase, cathepsin F, interalpha-trypsin inhibitor heavy chain 5, latent transforming growth factor beta-binding protein 4 and leukocyte-associated immunoglobulin-like receptor 1) overlapping between the top 30 DEPs with top-ranked P value and FC and top 30 proteins in PLS-DA VIP lists were acquired. Functional analysis revealed that the dysregulated proteins in the MOG group were primarily involved in complement and coagulation cascades, cell adhesion, axon guidance, and glycosphingolipid biosynthesis compared to the HC group. CONCLUSION The proteomic alterations in CSF samples from children with MOGAD identified in the current study might provide opportunities for developing novel biomarker candidates.
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Affiliation(s)
- Yi-Long Wang
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Meng-Ying Zhu
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Zhe-Feng Yuan
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Xiao-Yan Ren
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Xiao-Tong Guo
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Yi Hua
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Lu Xu
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Cong-Ying Zhao
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Li-Hua Jiang
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Xin Zhang
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Guo-Xia Sheng
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Pei-Fang Jiang
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Zheng-Yan Zhao
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China.
- Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou 310052, China.
| | - Feng Gao
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China.
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China.
- Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou 310052, China.
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Kordiš D, Turk V. Origin and Early Diversification of the Papain Family of Cysteine Peptidases. Int J Mol Sci 2023; 24:11761. [PMID: 37511529 PMCID: PMC10380794 DOI: 10.3390/ijms241411761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Peptidases of the papain family play a key role in protein degradation, regulated proteolysis, and the host-pathogen arms race. Although the papain family has been the subject of many studies, knowledge about its diversity, origin, and evolution in Eukaryota, Bacteria, and Archaea is limited; thus, we aimed to address these long-standing knowledge gaps. We traced the origin and expansion of the papain family with a phylogenomic analysis, using sequence data from numerous prokaryotic and eukaryotic proteomes, transcriptomes, and genomes. We identified the full complement of the papain family in all prokaryotic and eukaryotic lineages. Analysis of the papain family provided strong evidence for its early diversification in the ancestor of eukaryotes. We found that the papain family has undergone complex and dynamic evolution through numerous gene duplications, which produced eight eukaryotic ancestral paralogous C1A lineages during eukaryogenesis. Different evolutionary forces operated on C1A peptidases, including gene duplication, horizontal gene transfer, and gene loss. This study challenges the current understanding of the origin and evolution of the papain family and provides valuable insights into their early diversification. The findings of this comprehensive study provide guidelines for future structural and functional studies of the papain family.
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Affiliation(s)
- Dušan Kordiš
- Department of Molecular and Biomedical Sciences, J. Stefan Institute, 1000 Ljubljana, Slovenia
| | - Vito Turk
- Department of Biochemistry, Molecular and Structural Biology, J. Stefan Institute, 1000 Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia
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5
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Structure determinants defining the specificity of papain-like cysteine proteases. Comput Struct Biotechnol J 2022; 20:6552-6569. [DOI: 10.1016/j.csbj.2022.11.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/19/2022] [Accepted: 11/20/2022] [Indexed: 11/25/2022] Open
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6
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Expression signature, prognosis value and immune characteristics of cathepsin F in non-small cell lung cancer identified by bioinformatics assessment. BMC Pulm Med 2021; 21:420. [PMID: 34923982 PMCID: PMC8686609 DOI: 10.1186/s12890-021-01796-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/14/2021] [Indexed: 11/26/2022] Open
Abstract
Background In recent years, immunotherapies and targeted therapies contribute to population-level improvement in NSCLC cancer-specific survival, however, the two novel therapeutic options have mainly benefit patients containing mutated driven genes. Thus, to explore other potential genes related with immunity or targeted therapies may provide novel options to improve survival of lung cancer patients without mutated driven genes. CTSF is unique in human cysteine proteinases. Presently, CTSF has been detected in several cell lines of lung cancer, but its role in progression and prognosis of lung cancer remains unclear. Methods CTSF expression and clinical datasets of lung cancer patients were obtained from GTEx, TIMER, CCLE, THPA, and TCGA, respectively. Association of CTSF expression with clinicopathological parameters and prognosis of lung cancer patients was analyzed using UALCAN and Kaplan–Meier Plotter, respectively. LinkedOmics were used to analyze correlation between CTSF and CTSF co-expressed genes. Protein–protein interaction and gene–gene interaction were analyzed using STRING and GeneMANIA, respectively. Association of CTSF with molecular markers of immune cells and immunomodulators was analyzed with Immunedeconv and TISIDB, respectively. Results CTSF expression was currently only available for patients with NSCLC. Compared to normal tissues, CTSF was downregulated in NSCLC samples and high expressed CTSF was correlated with favorable prognosis of NSCLC. Additionally, CTSF expression was correlated with that of immune cell molecular markers and immunomodulators both in LUAD and LUSC. Noticeably, high expression of CTSF-related CTLA-4 was found to be associated with better OS of LUAD patients. Increased expression of CTSF-related LAG-3 was related with poor prognosis of LUAD patients while there was no association between CTSF-related PD-1/PD-L1 and prognosis of LUAD patients. Moreover, increased expression of CTSF-related CD27 was related with poor prognosis of LUAD patients while favorable prognosis of LUSC patients. Conclusions CTSF might play an anti-tumor effect via regulating immune response of NSCLC. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-021-01796-w.
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Sloan S, Jenvey C, Cairns C, Stear M. Cathepsin F of Teladorsagia circumcincta is a recently evolved cysteine protease. Evol Bioinform Online 2020; 16:1176934320962521. [PMID: 33100828 PMCID: PMC7549167 DOI: 10.1177/1176934320962521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 09/02/2020] [Indexed: 11/30/2022] Open
Abstract
Parasitic cysteine proteases are involved in parasite stage transition, invasion
of host tissues, nutrient uptake, and immune evasion. The cysteine protease
cathepsin F is the most abundant protein produced by fourth-stage larvae (L4) of
the nematode Teladorsagia circumcincta, while its transcript is
only detectable in L4 and adults. T. circumcincta cathepsin F
is a recently evolved cysteine protease that does not fall clearly into either
of the cathepsin L or F subfamilies. This protein exhibits characteristics of
both cathepsins F and L, and its phylogenetic relationship to its closest
homologs is distant, including proteins of closely related nematodes of the same
subfamily.
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Affiliation(s)
- Sarah Sloan
- AgriBio Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Caitlin Jenvey
- AgriBio Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Callum Cairns
- AgriBio Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Michael Stear
- AgriBio Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
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Cannalire R, Stefanelli I, Cerchia C, Beccari AR, Pelliccia S, Summa V. SARS-CoV-2 Entry Inhibitors: Small Molecules and Peptides Targeting Virus or Host Cells. Int J Mol Sci 2020; 21:ijms21165707. [PMID: 32784899 PMCID: PMC7460888 DOI: 10.3390/ijms21165707] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/07/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
The pandemic evolution of SARS-CoV-2 infection is forcing the scientific community to unprecedented efforts to explore all possible approaches against COVID-19. In this context, targeting virus entry is a promising antiviral strategy for controlling viral infections. The main strategies pursued to inhibit the viral entry are considering both the virus and the host factors involved in the process. Primarily, direct-acting antivirals rely on inhibition of the interaction between ACE2 and the receptor binding domain (RBD) of the Spike (S) protein or targeting the more conserved heptad repeats (HRs), involved in the membrane fusion process. The inhibition of host TMPRSS2 and cathepsins B/L may represent a complementary strategy to be investigated. In this review, we discuss the development entry inhibitors targeting the S protein, as well as the most promising host targeting strategies involving TMPRSS2 and CatB/L, which have been exploited so far against CoVs and other related viruses.
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Affiliation(s)
- Rolando Cannalire
- Department of Pharmacy, University of Napoli “Federico II”, via D. Montesano 49, 80131 Napoli, Italy; (R.C.); (I.S.); (C.C.); (S.P.)
| | - Irina Stefanelli
- Department of Pharmacy, University of Napoli “Federico II”, via D. Montesano 49, 80131 Napoli, Italy; (R.C.); (I.S.); (C.C.); (S.P.)
| | - Carmen Cerchia
- Department of Pharmacy, University of Napoli “Federico II”, via D. Montesano 49, 80131 Napoli, Italy; (R.C.); (I.S.); (C.C.); (S.P.)
| | | | - Sveva Pelliccia
- Department of Pharmacy, University of Napoli “Federico II”, via D. Montesano 49, 80131 Napoli, Italy; (R.C.); (I.S.); (C.C.); (S.P.)
| | - Vincenzo Summa
- Department of Pharmacy, University of Napoli “Federico II”, via D. Montesano 49, 80131 Napoli, Italy; (R.C.); (I.S.); (C.C.); (S.P.)
- Correspondence: ; Tel.: +39-081-678656
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Regulation of the Proteolytic Activity of Cysteine Cathepsins by Oxidants. Int J Mol Sci 2020; 21:ijms21061944. [PMID: 32178437 PMCID: PMC7139492 DOI: 10.3390/ijms21061944] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 12/21/2022] Open
Abstract
Besides their primary involvement in the recycling and degradation of proteins in endo-lysosomal compartments and also in specialized biological functions, cysteine cathepsins are pivotal proteolytic contributors of various deleterious diseases. While the molecular mechanisms of regulation via their natural inhibitors have been exhaustively studied, less is currently known about how their enzymatic activity is modulated during the redox imbalance associated with oxidative stress and their exposure resistance to oxidants. More specifically, there is only patchy information on the regulation of lung cysteine cathepsins, while the respiratory system is directly exposed to countless exogenous oxidants contained in dust, tobacco, combustion fumes, and industrial or domestic particles. Papain-like enzymes (clan CA, family C1, subfamily C1A) encompass a conserved catalytic thiolate-imidazolium pair (Cys25-His159) in their active site. Although the sulfhydryl group (with a low acidic pKa) is a potent nucleophile highly susceptible to chemical modifications, some cysteine cathepsins reveal an unanticipated resistance to oxidative stress. Besides an introductory chapter and peculiar attention to lung cysteine cathepsins, the purpose of this review is to afford a concise update of the current knowledge on molecular mechanisms associated with the regulation of cysteine cathepsins by redox balance and by oxidants (e.g., Michael acceptors, reactive oxygen, and nitrogen species).
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Processing and Maturation of Cathepsin C Zymogen: A Biochemical and Molecular Modeling Analysis. Int J Mol Sci 2019; 20:ijms20194747. [PMID: 31557781 PMCID: PMC6801622 DOI: 10.3390/ijms20194747] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/11/2019] [Accepted: 09/18/2019] [Indexed: 11/16/2022] Open
Abstract
Cysteine cathepsin C (CatC) is a ubiquitously expressed, lysosomal aminopeptidase involved in the activation of zymogens of immune-cell-associated serine proteinases (elastase, cathepsin G, proteinase 3, neutrophil serine proteinase 4, lymphocyte granzymes, and mast cell chymases). CatC is first synthetized as an inactive zymogen containing an intramolecular chain propeptide, the dimeric form of which is processed into the mature tetrameric form by proteolytic cleavages. A molecular modeling analysis of proCatC indicated that its propeptide displayed a similar fold to those of other lysosomal cysteine cathepsins, and could be involved in dimer formation. Our in vitro experiments revealed that human proCatC was processed and activated by CatF, CatK, and CatV in two consecutive steps of maturation, as reported for CatL and CatS previously. The unique positioning of the propeptide domains in the proCatC dimer complex allows this order of cleavages to be understood. The missense mutation Leu172Pro within the propeptide region associated with the Papillon-Lefèvre and Haim-Munk syndrome altered the proform stability as well as the maturation of the recombinant Leu172Pro proform.
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Tsuno H, Arito M, Suematsu N, Sato T, Hashimoto A, Matsui T, Omoteyama K, Sato M, Okamoto K, Tohma S, Kurokawa MS, Kato T. A proteomic analysis of serum-derived exosomes in rheumatoid arthritis. BMC Rheumatol 2018; 2:35. [PMID: 30886985 PMCID: PMC6390805 DOI: 10.1186/s41927-018-0041-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 10/18/2018] [Indexed: 12/29/2022] Open
Abstract
Background To understand the roles of serum exosomes in rheumatoid arthritis (RA), we comprehensively investigated the protein profiles of serum exosomes in patients with RA. Methods Exosomes were isolated from serum samples obtained from 33 patients (12 with active RA [aRA], 11 with inactive RA [iRA], 10 with osteoarthritis [OA]) and 10 healthy donors (HLs). Proteins extracted from the exosomes were separated by two-dimensional differential gel electrophoresis (2D-DIGE) and identified by mass spectrometry. Results In total, 204 protein spots were detected by 2D-DIGE. In the aRA, iRA, and OA groups, 24, 5, and 7 spots showed approximately ≥ ±1.3-fold intensity differences compared with the HL group, respectively. We were able to identify proteins in six protein spots. Among them, the protein spot identified as Toll-like receptor 3 (TLR3) showed approximately 6-fold higher intensity in the aRA group than in the other groups. Conclusions Patients with active RA possessed considerably different protein profiles of serum exosomes from patients with iRA, patients with OA, and healthy donors. The unique protein profile of serum exosomes, such as the possession of abundant TLR3 fragments, may reflect the pathophysiology of active RA. Electronic supplementary material The online version of this article (10.1186/s41927-018-0041-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hirotaka Tsuno
- 1Clinical Proteomics and Molecular Medicine, St. Marianna University Graduate School of Medicine, 2-16-1, Sugao, Miyamae, Kawasaki, Kanagawa 216-8511 Japan.,2Department of Rheumatology, National Hospital Organization Sagamihara National Hospital, 18-1, Sakuradai, Minami, Sagamihara, Kanagawa 252-0392 Japan
| | - Mitsumi Arito
- 1Clinical Proteomics and Molecular Medicine, St. Marianna University Graduate School of Medicine, 2-16-1, Sugao, Miyamae, Kawasaki, Kanagawa 216-8511 Japan
| | - Naoya Suematsu
- 1Clinical Proteomics and Molecular Medicine, St. Marianna University Graduate School of Medicine, 2-16-1, Sugao, Miyamae, Kawasaki, Kanagawa 216-8511 Japan
| | - Toshiyuki Sato
- 1Clinical Proteomics and Molecular Medicine, St. Marianna University Graduate School of Medicine, 2-16-1, Sugao, Miyamae, Kawasaki, Kanagawa 216-8511 Japan
| | - Atsushi Hashimoto
- 2Department of Rheumatology, National Hospital Organization Sagamihara National Hospital, 18-1, Sakuradai, Minami, Sagamihara, Kanagawa 252-0392 Japan
| | - Toshihiro Matsui
- 2Department of Rheumatology, National Hospital Organization Sagamihara National Hospital, 18-1, Sakuradai, Minami, Sagamihara, Kanagawa 252-0392 Japan
| | - Kazuki Omoteyama
- 1Clinical Proteomics and Molecular Medicine, St. Marianna University Graduate School of Medicine, 2-16-1, Sugao, Miyamae, Kawasaki, Kanagawa 216-8511 Japan
| | - Masaaki Sato
- 1Clinical Proteomics and Molecular Medicine, St. Marianna University Graduate School of Medicine, 2-16-1, Sugao, Miyamae, Kawasaki, Kanagawa 216-8511 Japan
| | - Kazuki Okamoto
- 5The Institute of Scientific and Industrial Research, Osaka University, 8-1, Mihogaoka, Osaka, Ibaraki 567-0047 Japan
| | - Shigeto Tohma
- 3National Hospital Organization Tokyo National Hospital, 3-1-1, Takeoka, Kiyose, Tokyo, 204-8585 Japan
| | - Manae S Kurokawa
- 4Disease Biomarker Analysis and Molecular Regulation, St. Marianna University Graduate School of Medicine, 2-16-1, Sugao, Miyamae, Kawasaki, Kanagawa 216-8511 Japan
| | - Tomohiro Kato
- 1Clinical Proteomics and Molecular Medicine, St. Marianna University Graduate School of Medicine, 2-16-1, Sugao, Miyamae, Kawasaki, Kanagawa 216-8511 Japan
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12
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Sérgio Alves Bueno P, Carina Biavatti D, Sandro Gularte Chiarello A, Aureliana Fassina V, Aparecida Fernandez M, Augusto Vicente Seixas F. The structure of viral cathepsin from Bombyx mori Nuclear Polyhedrosis Virus as a target against grasserie: docking and molecular dynamics simulations. J Biomol Struct Dyn 2018; 37:3607-3615. [PMID: 30198390 DOI: 10.1080/07391102.2018.1521344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The viral cathepsin from Bombyx mori Nuclear Polyhedrosis Virus (BmNPV-Cath) is a broad-spectrum protease that participates in the horizontal transmission of this virus in silkworm by facilitating solubilization of the integument of infected caterpillars. When a B. mori farm is attacked by BmNPV, there are significant sericultural losses because no drugs or therapies are available. In this work, the structure of viral cathepsin BmNPV-Cath was used as a target for virtual screening simulations, aiming to identify potential molecules that could be used to treat the infection. Virtual screening of the Natural Products library from the Zinc Database selected four molecules. Theoretical calculations of ΔGbinding by the molecular mechanics Poisson-Boltzmann surface analysis (MM-PBSA) method indicated that the molecule Zinc12888007 (Bm5) would have high affinity for the enzyme. The in vivo infection models of B. mori caterpillars with BmNPV showed that treatment with a dose of 100 μg Bm5 dissolved in Pluronic-F127 0.02% was able to reduce the mortality of caterpillars in 22.6%, however, it did not impede the liquefaction of dead bodies. Our results suggest a role of BmNPV-Cath in generating a pool of amino acids necessary for viral replication and indicate a mechanism to be exploited in the search for treatments for grasserie disease of the silkworm.
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Affiliation(s)
| | | | | | - Verônica Aureliana Fassina
- b Departamento de Biotecnologia, Genética e Biologia Celular , Universidade Estadual de Maringá , Maringá , Brazil
| | - Maria Aparecida Fernandez
- b Departamento de Biotecnologia, Genética e Biologia Celular , Universidade Estadual de Maringá , Maringá , Brazil
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13
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Guo H, Li Y, Zhang M, Li R, Li W, Lou J, Bao Z, Wang Y. Expression of Cathepsin F in response to bacterial challenges in Yesso scallop Patinopecten yessoensis. FISH & SHELLFISH IMMUNOLOGY 2018; 80:141-147. [PMID: 29879509 DOI: 10.1016/j.fsi.2018.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/31/2018] [Accepted: 06/02/2018] [Indexed: 06/08/2023]
Abstract
Cathepsin F is a unique papain cysteine proteinase with highly conserved structures: catalytic triad and a cystatin domain contained in the elongated N-terminal pro-region. It has been reported that cathepsin F is associated with the establishment of innate immune in several vertebrate including fish in aquaculture, but not known in bivalves. In this study, we firstly identified and characterized cathepsin F in the Yesso scallop (Patinopecten yessoensis). The protein structural and phylogenetic analyses were then conducted to determine its identity and evolutionary position. We've also investigated the expression levels of cathepsin F gene at different embryonic developmental stages, in healthy adult tissues and especially in the hemocytes and hepatopancreas after Gram-positive (Micrococcus luteus) and negative (Vibrio anguillarum) challenges using quantitative real-time PCR (qPCR). Cathepsin F was significantly up-regulated 3 h after infection of V. anguillarum in hemocytes, suggesting its participation in immune response. Our findings have provided strong evidence that cathepsin F may be a good target for enhancing the immune activity in Yesso scallop.
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Affiliation(s)
- Haobing Guo
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Yangping Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Meiwei Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Ruojiao Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Wanru Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Jiarun Lou
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Zhenmin Bao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yangfan Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
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14
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Cysteine cathepsins as a prospective target for anticancer therapies-current progress and prospects. Biochimie 2018; 151:85-106. [PMID: 29870804 DOI: 10.1016/j.biochi.2018.05.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 05/31/2018] [Indexed: 02/08/2023]
Abstract
Cysteine cathepsins (CTS), being involved in both physiological and pathological processes, play an important role in the human body. During the last 30 years, it has been shown that CTS are highly upregulated in a wide variety of cancer types although they have received a little attention as a potential therapeutic target as compared to serine or metalloproteinases. Studies on the increasing problem of neoplastic progression have revealed that secretion of cell-surface- and intracellular cysteine proteases is aberrant in tumor cells and has an impact on their growth, invasion, and metastasis by taking part in tumor angiogenesis, in apoptosis, and in events of inflammatory and immune responses. Considering the role of CTS in carcinogenesis, inhibition of these enzymes becomes an attractive strategy for cancer therapy. The downregulation of natural CTS inhibitors (CTSsis), such as cystatins, observed in various types of cancer, supports this claim. The intention of this review is to highlight the relationship of CTS with cancer and to present illustrations that explain how some of their inhibitors affect processes related to neoplastic progression.
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15
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Jain V, Sharma A, Singh G, Yogavel M, Sharma A. Structure-Based Targeting of Orthologous Pathogen Proteins Accelerates Antiparasitic Drug Discovery. ACS Infect Dis 2017; 3:281-292. [PMID: 28195698 DOI: 10.1021/acsinfecdis.6b00181] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Parasitic diseases caused by eukaryotic pathogens impose significant health and economic burden worldwide. The level of research funding available for many parasitic diseases is insufficient in relation to their adverse social and economic impact. In this article, we discuss that extant 3D structural data on protein-inhibitor complexes can be harnessed to accelerate drug discovery against many related pathogens. Assessment of sequence conservation within drug/inhibitor-binding residues in enzyme-inhibitor complexes can be leveraged to predict and validate both new lead compounds and their molecular targets in multiple parasitic diseases. Hence, structure-based targeting of orthologous pathogen proteins accelerates the discovery of new antiparasitic drugs. This approach offers significant benefits for jumpstarting the discovery of new lead compounds and their molecular targets in diverse human, livestock, and plant pathogens.
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Affiliation(s)
- Vitul Jain
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Road, New Delhi 110067, India
| | - Arvind Sharma
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Road, New Delhi 110067, India
| | - Gajinder Singh
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Road, New Delhi 110067, India
| | - Manickam Yogavel
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Road, New Delhi 110067, India
| | - Amit Sharma
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Road, New Delhi 110067, India
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16
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A Novel Yeast Surface Display Method for Large-Scale Screen Inhibitors of Sortase A. Bioengineering (Basel) 2017; 4:bioengineering4010006. [PMID: 28952485 PMCID: PMC5590430 DOI: 10.3390/bioengineering4010006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 12/27/2016] [Accepted: 01/15/2017] [Indexed: 11/17/2022] Open
Abstract
Fluorescence resonance energy transfer substrates of sortase A are too expensive to be used to roughly screen high-throughput sortase A inhibitors. This makes therapeutic strategies difficult to realize in a clinical therapeutic use. Instead, we design here an LPETG-EGFP (leucine, proline, glutamic, threonine and glycine-enhanced green fluorescence) protein displayed on a yeast surface as a substrate by adaptively reducing the cost. We do this by optimizing the induction conditions of sortase A expression in Escherichia coli DE3(BL21) and catalyzing LPETG proteins, which are displayed on surface of Pichia pastoris. Different expression conditions of sortase A include: induction temperature (22 °C, 28 °C, 37 °C and 40 °C), induction time (4 h, 5 h, 6 h and 7 h) and induction concentration of isopropyl β-d-thiogalactoside IPTG (0.25 mmol/L, 0.5 mmol/L, 1 mmol/L, and 2 mmol/L). The fluorescence change of the LPETG-EGFP protein on the surface of P. pastoris over time was detected by flow cytometry and fluorescence spectrophotometry, and then the sensitivities of the two methods were compared. Using berberine chloride as an inhibitor, the activity of sortase A was investigated with the substrates of LPETG-EGFP protein, and compared to Dabcyl-QALPETGEE-Edans. A high yield of sortase A was achieved by inducing 1.0 mmol/L IPTG at 28 °C for 6 h. The intensity of green fluorescence of substrates displayed on the yeast surface was increased over time, while the stability was decreased slightly. Both fluorescence spectrophotometery and flow cytometry were fit for detection because of their high sensitivity. We utilized two different substrates of sortase A to investigate sortase A activity, which resulted in the increase of fluorescence intensity with respect to the increased time of growth. However, the method with Dabcyl-QALPETGEE-Edans as its substrate was more robust. Thus, the method described in this paper is a simple and cheap method which is very suitable for high-throughput analysis, but the conventional method is much more sensitive. The method described in this paper is expected to lead to large-scale screening of sortase A inhibitors which can be used to decrease the risk of drug resistance development.
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17
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Stoka V, Turk V, Turk B. Lysosomal cathepsins and their regulation in aging and neurodegeneration. Ageing Res Rev 2016; 32:22-37. [PMID: 27125852 DOI: 10.1016/j.arr.2016.04.010] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/12/2016] [Accepted: 04/23/2016] [Indexed: 02/07/2023]
Abstract
Lysosomes and lysosomal hydrolases, including the cathepsins, have been shown to change their properties with aging brain a long time ago, although their function was not really understood. The first biochemical and clinical studies were followed by a major expansion in the last 20 years with the development of animal disease models and new approaches leading to a major advancement of understanding of the role of physiological and degenerative processes in the brain at the molecular level. This includes the understanding of the major role of autophagy and the cathepsins in a number of diseases, including its critical role in the neuronal ceroid lipofuscinosis. Similarly, cathepsins and some other lysosomal proteases were shown to have important roles in processing and/or degradation of several important neuronal proteins, thereby having either neuroprotective or harmful roles. In this review, we discuss lysosomal cathepsins and their regulation with the focus on cysteine cathepsins and their endogenous inhibitors, as well as their role in several neurodegenerative diseases.
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Affiliation(s)
- Veronika Stoka
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Jamova 39, Sl-1000 Ljubljana, Slovenia; J. Stefan International Postgraduate School, Jamova 39, Sl-1000 Ljubljana, Slovenia.
| | - Vito Turk
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Jamova 39, Sl-1000 Ljubljana, Slovenia; J. Stefan International Postgraduate School, Jamova 39, Sl-1000 Ljubljana, Slovenia
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Jamova 39, Sl-1000 Ljubljana, Slovenia; Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, Sl-1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Sl-1000 Ljubljana, Slovenia.
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18
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Lecaille F, Lalmanach G, Andrault PM. Antimicrobial proteins and peptides in human lung diseases: A friend and foe partnership with host proteases. Biochimie 2015; 122:151-68. [PMID: 26341472 DOI: 10.1016/j.biochi.2015.08.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 08/31/2015] [Indexed: 12/20/2022]
Abstract
Lung antimicrobial proteins and peptides (AMPs) are major sentinels of innate immunity by preventing microbial colonization and infection. Nevertheless bactericidal activity of AMPs against Gram-positive and Gram-negative bacteria is compromised in patients with chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF) and asthma. Evidence is accumulating that expression of harmful human serine proteases, matrix metalloproteases and cysteine cathepsins is markedely increased in these chronic lung diseases. The local imbalance between proteases and protease inhibitors compromises lung tissue integrity and function, by not only degrading extracellular matrix components, but also non-matrix proteins. Despite the fact that AMPs are somewhat resistant to proteolytic degradation, some human proteases cleave them efficiently and impair their antimicrobial potency. By contrast, certain AMPs may be effective as antiproteases. Host proteases participate in concert with bacterial proteases in the degradation of key innate immunity peptides/proteins and thus may play immunomodulatory activities during chronic lung diseases. In this context, the present review highlights the current knowledge and recent discoveries on the ability of host enzymes to interact with AMPs, providing a better understanding of the role of human proteases in innate host defense.
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Affiliation(s)
- Fabien Lecaille
- INSERM, UMR 1100, Pathologies Respiratoires: Protéolyse et Aérosolthérapie, Centre d'Etude des Pathologies Respiratoires, Equipe 2: « Mécanismes Protéolytiques dans l'Inflammation », Université François Rabelais, F-37032 Tours cedex, France.
| | - Gilles Lalmanach
- INSERM, UMR 1100, Pathologies Respiratoires: Protéolyse et Aérosolthérapie, Centre d'Etude des Pathologies Respiratoires, Equipe 2: « Mécanismes Protéolytiques dans l'Inflammation », Université François Rabelais, F-37032 Tours cedex, France
| | - Pierre-Marie Andrault
- INSERM, UMR 1100, Pathologies Respiratoires: Protéolyse et Aérosolthérapie, Centre d'Etude des Pathologies Respiratoires, Equipe 2: « Mécanismes Protéolytiques dans l'Inflammation », Université François Rabelais, F-37032 Tours cedex, France
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19
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Schmitz J, Furtmann N, Ponert M, Frizler M, Löser R, Bartz U, Bajorath J, Gütschow M. Active Site Mapping of Human Cathepsin F with Dipeptide Nitrile Inhibitors. ChemMedChem 2015; 10:1365-77. [PMID: 26119278 DOI: 10.1002/cmdc.201500151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Indexed: 11/09/2022]
Abstract
Cleavage of the invariant chain is the key event in the trafficking pathway of major histocompatibility complex class II. Cathepsin S is the major processing enzyme of the invariant chain, but cathepsin F acts in macrophages as its functional synergist which is as potent as cathepsin S in invariant chain cleavage. Dedicated low-molecular-weight inhibitors for cathepsin F have not yet been developed. An active site mapping with 52 dipeptide nitriles, reacting as covalent-reversible inhibitors, was performed to draw structure-activity relationships for the non-primed binding region of human cathepsin F. In a stepwise process, new compounds with optimized fragment combinations were designed and synthesized. These dipeptide nitriles were evaluated on human cysteine cathepsins F, B, L, K and S. Compounds 10 (N-(4-phenylbenzoyl)-leucylglycine nitrile) and 12 (N-(4-phenylbenzoyl)leucylmethionine nitrile) were found to be potent inhibitors of human cathepsin F, with Ki values <10 nM. With all dipeptide nitriles from our study, a 3D activity landscape was generated to visualize structure-activity relationships for this series of cathepsin F inhibitors.
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Affiliation(s)
- Janina Schmitz
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany).,Department of Natural Sciences, University of Applied Sciences Bonn-Rhein-Sieg von-Liebig-Straße 20, 53359 Rheinbach (Germany)
| | - Norbert Furtmann
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany).,Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, University of Bonn, Dahlmannstraße 2, 53113 Bonn (Germany)
| | - Moritz Ponert
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany)
| | - Maxim Frizler
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany)
| | - Reik Löser
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany).,Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328 Dresden (Germany)
| | - Ulrike Bartz
- Department of Natural Sciences, University of Applied Sciences Bonn-Rhein-Sieg von-Liebig-Straße 20, 53359 Rheinbach (Germany)
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, University of Bonn, Dahlmannstraße 2, 53113 Bonn (Germany)
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany).
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20
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Cascioferro S, Totsika M, Schillaci D. Sortase A: An ideal target for anti-virulence drug development. Microb Pathog 2014; 77:105-12. [DOI: 10.1016/j.micpath.2014.10.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 10/08/2014] [Accepted: 10/15/2014] [Indexed: 10/24/2022]
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21
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Leite NR, Faro AR, Dotta MAO, Faim LM, Gianotti A, Silva FH, Oliva G, Thiemann OH. The crystal structure of the cysteine protease Xylellain from Xylella fastidiosa reveals an intriguing activation mechanism. FEBS Lett 2013; 587:339-44. [PMID: 23333295 DOI: 10.1016/j.febslet.2013.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 12/21/2012] [Accepted: 01/03/2013] [Indexed: 10/27/2022]
Abstract
Xylella fastidiosa is responsible for a wide range of economically important plant diseases. We report here the crystal structure and kinetic data of Xylellain, the first cysteine protease characterized from the genome of the pathogenic X. fastidiosa strain 9a5c. Xylellain has a papain-family fold, and part of the N-terminal sequence blocks the enzyme active site, thereby mediating protein activity. One novel feature identified in the structure is the presence of a ribonucleotide bound outside the active site. We show that this ribonucleotide plays an important regulatory role in Xylellain enzyme kinetics, possibly functioning as a physiological mediator.
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Affiliation(s)
- Ney Ribeiro Leite
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP 13566-590, Brazil
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22
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Smith KR, Dahl HHM, Canafoglia L, Andermann E, Damiano J, Morbin M, Bruni AC, Giaccone G, Cossette P, Saftig P, Grötzinger J, Schwake M, Andermann F, Staropoli JF, Sims KB, Mole SE, Franceschetti S, Alexander NA, Cooper JD, Chapman HA, Carpenter S, Berkovic SF, Bahlo M. Cathepsin F mutations cause Type B Kufs disease, an adult-onset neuronal ceroid lipofuscinosis. Hum Mol Genet 2013; 22:1417-23. [PMID: 23297359 DOI: 10.1093/hmg/dds558] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Kufs disease, an adult-onset neuronal ceroid lipofuscinosis, is challenging to diagnose and genetically heterogeneous. Mutations in CLN6 were recently identified in recessive Kufs disease presenting as progressive myoclonus epilepsy (Type A), whereas the molecular basis of cases presenting with dementia and motor features (Type B) is unknown. We performed genome-wide linkage mapping of two families with recessive Type B Kufs disease and identified a single region on chromosome 11 to which both families showed linkage. Exome sequencing of five samples from the two families identified homozygous and compound heterozygous missense mutations in CTSF within this linkage region. We subsequently sequenced CTSF in 22 unrelated individuals with suspected recessive Kufs disease, and identified an additional patient with compound heterozygous mutations. CTSF encodes cathepsin F, a lysosomal cysteine protease, dysfunction of which is a highly plausible candidate mechanism for a storage disorder like ceroid lipofuscinosis. In silico modeling suggested the missense mutations would alter protein structure and function. Moreover, re-examination of a previously published mouse knockout of Ctsf shows that it recapitulates the light and electron-microscopic pathological features of Kufs disease. Although CTSF mutations account for a minority of cases of type B Kufs, CTSF screening should be considered in cases with early-onset dementia and may avoid the need for invasive biopsies.
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Affiliation(s)
- Katherine R Smith
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne 3052, Australia
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23
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Frizler M, Schmitz J, Schulz-Fincke AC, Gütschow M. Selective nitrile inhibitors to modulate the proteolytic synergism of cathepsins S and F. J Med Chem 2012; 55:5982-6. [PMID: 22686657 DOI: 10.1021/jm300734k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of dipeptide nitriles with different P3 substituents was designed to explore the S3 binding pocket of cathepsin S. Racemic 7-16 and the enantiopure derivative (R)-22 proved to be potent inhibitors of human cathepsin S and exhibited notable selectivity over human cathepsins L, K, and B. Inhibition of cathepsin F, the functional synergist of cathepsin S, was not observed. The azadipeptide analogue of 22, compound 26, was highly potent but nonselective.
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Affiliation(s)
- Maxim Frizler
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
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24
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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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25
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26
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Kasabova M, Saidi A, Naudin C, Sage J, Lecaille F, Lalmanach G. Cysteine Cathepsins: Markers and Therapy Targets in Lung Disorders. Clin Rev Bone Miner Metab 2011. [DOI: 10.1007/s12018-011-9094-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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27
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Mendieta L, Picó A, Tarragó T, Teixidó M, Castillo M, Rafecas L, Moyano A, Giralt E. Novel peptidyl aryl vinyl sulfones as highly potent and selective inhibitors of cathepsins L and B. ChemMedChem 2011; 5:1556-67. [PMID: 20652927 DOI: 10.1002/cmdc.201000109] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Herein we present the design, synthesis, and evaluation of a structurally novel library of 20 peptidyl 3-aryl vinyl sulfones as inhibitors of cathepsins L and B. The building blocks, described here for the first time, were synthesized in a highly efficient and enantioselective manner, starting from 3-aryl-substituted allyl alcohols. The corresponding vinyl sulfones were prepared by a new approach, based on a combination of solid-phase peptide synthesis using the Fmoc/tBu strategy, followed by solution-phase coupling to the corresponding (R)-3-amino-3-aryl vinyl sulfones as trifluoroacetate salts. The inhibitory activity of the resulting compounds against cathepsins L and B was evaluated, and the compound exhibiting the best activity was selected for enzymatic characterization. Finally, docking studies were performed in order to identify key structural features of the aryl substituent.
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Affiliation(s)
- Laura Mendieta
- Institute for Research in Biomedicine of Barcelona, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
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Ahn SJ, Kim NY, Seo JS, Je JE, Sung JH, Lee SH, Kim MS, Kim JK, Chung JK, Lee HH. Molecular cloning, mRNA expression and enzymatic characterization of cathepsin F from olive flounder (Paralichthys olivaceus). Comp Biochem Physiol B Biochem Mol Biol 2009; 154:211-20. [DOI: 10.1016/j.cbpb.2009.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 06/11/2009] [Accepted: 06/11/2009] [Indexed: 11/29/2022]
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Pinlaor P, Kaewpitoon N, Laha T, Sripa B, Kaewkes S, Morales ME, Mann VH, Parriott SK, Suttiprapa S, Robinson MW, To J, Dalton JP, Loukas A, Brindley PJ. Cathepsin F cysteine protease of the human liver fluke, Opisthorchis viverrini. PLoS Negl Trop Dis 2009; 3:e398. [PMID: 19308250 PMCID: PMC2654340 DOI: 10.1371/journal.pntd.0000398] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Accepted: 02/25/2009] [Indexed: 01/30/2023] Open
Abstract
Background The liver fluke Opisthorchis viverrini is classified as a class I carcinogen due to the association between cholangiocarcinoma and chronic O. viverrini infection. During its feeding activity within the bile duct, the parasite secretes several cathepsin F cysteine proteases that may induce or contribute to the pathologies associated with hepatobiliary abnormalities. Methodology/Principal Findings Here, we describe the cDNA, gene organization, phylogenetic relationships, immunolocalization, and functional characterization of the cathepsin F cysteine protease gene, here termed Ov-cf-1, from O. viverrini. The full length mRNA of 1020 nucleotides (nt) encoded a 326 amino acid zymogen consisting of a predicted signal peptide (18 amino acids, aa), prosegment (95 aa), and mature protease (213 aa). BLAST analysis using the Ov-CF-1 protein as the query revealed that the protease shared identity with cathepsin F-like cysteine proteases of other trematodes, including Clonorchis sinensis (81%), Paragonimus westermani (58%), Schistosoma mansoni and S. japonicum (52%), and with vertebrate cathepsin F (51%). Transcripts encoding the protease were detected in all developmental stages that parasitize the mammalian host. The Ov-cf-1 gene, of ∼3 kb in length, included seven exons interrupted by six introns; the exons ranged from 69 to 267 bp in length, the introns from 43 to 1,060 bp. The six intron/exon boundaries of Ov-cf-1 were conserved with intron/exon boundaries in the human cathepsin F gene, although the gene structure of human cathepsin F is more complex. Unlike Ov-CF-1, human cathepsin F zymogen includes a cystatin domain in the prosegment region. Phylogenetic analysis revealed that the fluke, human, and other cathepsin Fs branched together in a clade discrete from the cathepsin L cysteine proteases. A recombinant Ov-CF-1 zymogen that displayed low-level activity was expressed in the yeast Pichia pastoris. Although the recombinant protease did not autocatalytically process and activate to a mature enzyme, trans-processing by Fasciola hepatica cathepsin L cleaved the prosegment of Ov-CF-1, releasing a mature cathepsin F with activity against the peptide Z-Phe-Arg-NHMec >50 times that of the zymogen. Immunocytochemistry using antibodies raised against the recombinant enzyme showed that Ov-CF-1 is expressed in the gut of the mature hermaphroditic fluke and also in the reproductive structures, including vitelline glands, egg, and testis. Ov-CF-1 was detected in bile duct epithelial cells surrounding the flukes several weeks after infection of hamsters with O. viverrini and, in addition, had accumulated in the secondary (small) bile ducts where flukes cannot reach due to their large size. Conclusions/Significance A cathepsin F cysteine protease of the human liver fluke O. viverrini has been characterized at the gene and protein level. Secretion of this protease may contribute to the hepatobiliary abnormalities, including cholangiocarcinogenesis, observed in individuals infected with this parasite. Opisthorchiasis, oriental liver fluke infection, is a food-borne parasitic disease that afflicts millions of residents in northern Thailand and Laos. Related infections occur in North Asia, including China and Korea. This kind of liver fluke infection is the consequence of eating certain uncooked or undercooked freshwater fish contaminated with the larvae of the parasite Opisthorchis viverrini. Whereas the infection can cause disease in the bile ducts and liver, infection with the oriental fluke can lead to the development of a liver cancer, cholangiocarcinoma (bile duct cancer). Our recent studies have begun to focus on products and metabolites from the parasite that are carcinogenic. Many proteolytic enzymes are known to be secreted by parasites. This report centers on a specific category of protease, termed cathepsin F. We determined here that O. viverrini expresses a cathepsin F in its gut and in other organs. In the liver fluke, cathepsin F likely plays a role in digesting ingested human cells. The gene encoding the parasite enzyme shows evolutionary relatedness to a similar gene in humans. The fluke cathepsin F also is released from the parasite into livers of infected mammals, where it appears to contribute to inflammation surrounding the parasite. In this regard, it may be involved in early events that lead to bile duct cancer.
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Affiliation(s)
- Porntip Pinlaor
- Department of Pathology, Khon Kaen University, Khon Kaen, Thailand
- Faculty of Allied Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
- Department of Tropical Medicine, Tulane University Health Sciences Center, New Orleans, Louisiana, United States of America
| | | | - Thewarach Laha
- Department of Parasitology, Khon Kaen University, Khon Kaen, Thailand
| | - Banchob Sripa
- Department of Pathology, Khon Kaen University, Khon Kaen, Thailand
- * E-mail: (BS); (PJR)
| | - Sasithorn Kaewkes
- Department of Parasitology, Khon Kaen University, Khon Kaen, Thailand
| | - Maria E. Morales
- Department of Tropical Medicine, Tulane University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Victoria H. Mann
- Department of Tropical Medicine, Tulane University Health Sciences Center, New Orleans, Louisiana, United States of America
- Department of Microbiology, Immunology & Tropical Medicine, George Washington University Medical Center, Washington, D.C., United States of America
| | - Sandi K. Parriott
- Department of Tropical Medicine, Tulane University Health Sciences Center, New Orleans, Louisiana, United States of America
- Department of Microbiology, Immunology & Tropical Medicine, George Washington University Medical Center, Washington, D.C., United States of America
| | - Sutas Suttiprapa
- Department of Pathology, Khon Kaen University, Khon Kaen, Thailand
- Department of Microbiology, Immunology & Tropical Medicine, George Washington University Medical Center, Washington, D.C., United States of America
| | - Mark W. Robinson
- Institute for the Biotechnology of Infectious Diseases, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Joyce To
- Institute for the Biotechnology of Infectious Diseases, University of Technology Sydney, Sydney, New South Wales, Australia
| | - John P. Dalton
- Institute for the Biotechnology of Infectious Diseases, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Alex Loukas
- Division of Infectious Diseases, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Paul J. Brindley
- Department of Tropical Medicine, Tulane University Health Sciences Center, New Orleans, Louisiana, United States of America
- Department of Microbiology, Immunology & Tropical Medicine, George Washington University Medical Center, Washington, D.C., United States of America
- * E-mail: (BS); (PJR)
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Mihelic M, Dobersek A, Guncar G, Turk D. Inhibitory fragment from the p41 form of invariant chain can regulate activity of cysteine cathepsins in antigen presentation. J Biol Chem 2008; 283:14453-60. [PMID: 18362148 DOI: 10.1074/jbc.m801283200] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cysteine cathepsins play an indispensable role in proteolytic processing of the major histocompatibility complex class II-associated invariant chain (Ii) and foreign antigens in a number of antigen presenting cells. Previously it was shown that a fragment of 64 residues present in the p41 form of the Ii (p41 fragment) selectively inhibits the endopeptidase cathepsin L, whereas the activity of cathepsin S remains unaffected. Comparison of structures indicated that the selectivity of interactions between cysteine cathepsins and the p41 fragment is far from being understood and requires further investigation. The p41 fragment has now been shown also to inhibit human cathepsins V, K, and F (also, presumably, O) and mouse cathepsin L with K(i) values in the low nanomolar range. These K(i) values are sufficiently low to ensure complex formation at physiological concentrations. In addition we have found that the p41 fragment can inhibit cathepsin S too. These findings suggest that regulation of the proteolytic activity of most of the cysteine cathepsins by the p41 fragment is an important and widespread control mechanism of antigen presentation.
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Affiliation(s)
- Marko Mihelic
- Department of Biochemistry and Molecular and Structural Biology, J Stefan Institute, Ljubljana, Slovenia
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31
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Barrett DG, Catalano JG, Deaton DN, Long ST, McFadyen RB, Miller AB, Miller LR, Samano V, Tavares FX, Wells-Knecht KJ, Wright LL, Zhou HQQ. Acyclic, orally bioavailable ketone-based cathepsin K inhibitors. Bioorg Med Chem Lett 2006; 17:22-7. [PMID: 17157021 DOI: 10.1016/j.bmcl.2006.10.102] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Revised: 10/03/2006] [Accepted: 10/04/2006] [Indexed: 11/22/2022]
Abstract
Starting from a potent ketone-based inhibitor with poor drug properties, incorporation of P(2)-P(3) elements from a ketoamide-based inhibitor led to the identification of a hybrid series of ketone-based cathepsin K inhibitors with better oral bioavailability than the starting ketone.
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Affiliation(s)
- David G Barrett
- Department of Medicinal Chemistry, GlaxoSmithKline, Research Triangle Park, NC 27709, USA
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32
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Bratkovic T, Lunder M, Popovic T, Kreft S, Turk B, Strukelj B, Urleb U. Affinity selection to papain yields potent peptide inhibitors of cathepsins L, B, H, and K. Biochem Biophys Res Commun 2005; 332:897-903. [PMID: 15913550 DOI: 10.1016/j.bbrc.2005.05.028] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2005] [Accepted: 05/09/2005] [Indexed: 11/24/2022]
Abstract
Endogenous cysteine proteases were given much attention lately, as their role in a variety of pathophysiological disorders became evident. Amongst them cathepsins, which are thought to be implicated in mediation of osteoporosis, cancer progression, atherosclerosis, and many other conditions, are of considerable interest as drug targets. In the presented work, papain was chosen as a model cysteine protease and panning protocol was optimized for selection of papain-binding phage-displayed peptides from a commercially available combinatorial peptide library. Different selection strategies were applied in order to select high-affinity binders. Ultimately, five cyclic peptides (CNWAAGYNCGGGS-NH2, CWSMMGFQCGGGS-NH2, CWEWGGWHCGGSS-OH, CNWTLGGYKCGGGS-NH2 (all cyclized through formation of intramolecular disulphide bond), and GNWTLGGYKGG (cyclized head-to-tail)) were synthesized and tested for inhibitory activity towards papain and human cathepsins L, B, H, and K. The peptides possess inhibitory constants in the low micromolar to mid-nanomolar range and exhibit certain selectivity for different lysosomal cysteine proteases included in this study.
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Affiliation(s)
- Tomaz Bratkovic
- Faculty of Pharmacy, Department of Pharmaceutical Biology, University of Ljubljana, Askerceva 7, SI-1000 Ljubljana, Slovenia.
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33
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Barrett DG, Catalano JG, Deaton DN, Long ST, McFadyen RB, Miller AB, Miller LR, Wells-Knecht KJ, Wright LL. A structural screening approach to ketoamide-based inhibitors of cathepsin K. Bioorg Med Chem Lett 2005; 15:2209-13. [PMID: 15837295 DOI: 10.1016/j.bmcl.2005.03.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2005] [Revised: 03/04/2005] [Accepted: 03/07/2005] [Indexed: 11/23/2022]
Abstract
Several novel ketoamide-based inhibitors of cathepsin K have been identified. Starting from a modestly potent inhibitor, structural screening of P2 elements led to 100-fold enhancements in inhibitory activity. Modifications to one of these leads resulted in an orally bioavailable cathepsin K inhibitor.
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Affiliation(s)
- David G Barrett
- Department of Medicinal Chemistry, GlaxoSmithKline, Research Triangle Park, North Carolina 27709, USA
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34
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Quibell M, Benn A, Flinn N, Monk T, Ramjee M, Wang Y, Watts J. Bicyclic peptidomimetic tetrahydrofuro[3,2-b]pyrrol-3-one and hexahydrofuro[3,2-b]pyridine-3-one based scaffolds: synthesis and cysteinyl proteinase inhibition. Bioorg Med Chem 2005; 12:5689-710. [PMID: 15465346 DOI: 10.1016/j.bmc.2004.07.054] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2004] [Accepted: 07/23/2004] [Indexed: 12/13/2022]
Abstract
A stereoselective synthesis of (3aS,6aR)-tetrahydrofuro[3,2-b]pyrrol-3-ones and (3aS,7aR)-hexahydrofuro[3,2-b]pyridine-3-ones has been developed through Fmoc protected scaffolds 12 and 13. A key design element within these novel bicyclic scaffolds, in particular the 5,5-fused system, was the inherent stability of the cis-fused geometry in comparison to that of the corresponding trans-fused. Since the bridgehead stereocentre situated beta to the ketone was of a fixed and stable configuration, the fact that cis ring fusion is both kinetically and thermodynamically stable with respect to trans ring fusion provides chiral stability to the bridgehead stereocentre that is situated alpha to the ketone. To exemplify this principle, building blocks 12 and 13 were designed, prepared and utilised in a solid phase combinatorial synthesis of peptidomimetic inhibitors 10, 45a-e, 11 and 46. Both series were chirally stable with 5,5-series 10 and 45a-e exhibiting potent in vitro activity against a range of CAC1 cysteinyl proteinases. Compound 10, a potent and selective inhibitor of cathepsin K, possessed good primary DMPK properties along with promising activity in an in vitro cell-based human osteoclast assay of bone resorption.
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Affiliation(s)
- Martin Quibell
- Amura Therapeutics Limited, Incenta House, Horizon Park, Barton Road, Comberton, Cambridge CB3 7AJ, UK.
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35
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Rossi A, Deveraux Q, Turk B, Sali A. Comprehensive search for cysteine cathepsins in the human genome. Biol Chem 2005; 385:363-72. [PMID: 15195995 DOI: 10.1515/bc.2004.040] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Our study was aimed at examinating whether or not the human genome encodes for previously unreported cysteine cathepsins. To this end, we used analyses of the genome sequence and mRNA expression levels. The program TBLASTN was employed to scan the draft sequence of the human genome for the 11 known cysteine cathepsins. The cathepsin-like segments in the genome were inspected, filtered, and annotated. In addition to the known cysteine cathepsins, the scan identified three pseudogenes, closely related to cathepsin L, on chromosome 10, as well as two remote homologs, tubulointerstitial protein antigen and tubulointerstitial protein antigen-related protein. No new members of the family were identified. mRNA expression profiles for 10 known human cysteine cathepsins showed varying expression levels in 46 different human tissues and cell lines. No expression of any of the three cathepsin L-like pseudogenes was found. Based on these results, it is likely that to date all human cysteine cathepsins are known.
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Affiliation(s)
- Andrea Rossi
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA 94143-2240, USA
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36
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Barrett DG, Catalano JG, Deaton DN, Hassell AM, Long ST, Miller AB, Miller LR, Shewchuk LM, Wells-Knecht KJ, Willard DH, Wright LL. Potent and selective P2–P3 ketoamide inhibitors of cathepsin K with good pharmacokinetic properties via favorable P1′, P1, and/or P3 substitutions. Bioorg Med Chem Lett 2004; 14:4897-902. [PMID: 15341947 DOI: 10.1016/j.bmcl.2004.07.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2004] [Revised: 07/13/2004] [Accepted: 07/17/2004] [Indexed: 10/26/2022]
Abstract
A series of ketoamides were synthesized and evaluated for inhibitory activity against cathepsin K. Exploration of the interactions between achiral P(2) substituents and the cysteine protease based on molecular modelling suggestions resulted in potent cathepsin K inhibitors that demonstrated high selectivity versus cathepsins B, H, and L. Subsequent modifications of the P(3), P(1), and P(1') moieties afforded orally bioavailable inhibitors.
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Affiliation(s)
- David G Barrett
- Department of Medicinal Chemistry, GlaxoSmithKline, Research Triangle Park, NC 27709, USA
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37
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Barrett DG, Catalano JG, Deaton DN, Long ST, Miller LR, Tavares FX, Wells-Knecht KJ, Wright LL, Zhou HQQ. Orally bioavailable small molecule ketoamide-based inhibitors of cathepsin K. Bioorg Med Chem Lett 2004; 14:2543-6. [PMID: 15109647 DOI: 10.1016/j.bmcl.2004.02.085] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2004] [Revised: 02/23/2004] [Accepted: 02/26/2004] [Indexed: 10/26/2022]
Abstract
An orally available series of ketoamide-based inhibitors of cathepsin K has been identified. Starting from a potent inhibitor with poor oral bioavailability, modifications to P1 and P1' elements led to enhancements in solubility and permeability. These improvements resulted in orally available cathepsin K inhibitors.
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Affiliation(s)
- David G Barrett
- Department of Medicinal Chemistry, GlaxoSmithKline, Research Triangle Park, NC 27709, USA
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38
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Catalano JG, Deaton DN, Long ST, McFadyen RB, Miller LR, Payne JA, Wells-Knecht KJ, Wright LL. Design of small molecule ketoamide-based inhibitors of cathepsin K. Bioorg Med Chem Lett 2004; 14:719-22. [PMID: 14741275 DOI: 10.1016/j.bmcl.2003.11.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A novel series of ketoamide-based inhibitors of cathepsin K has been identified. Modifications to P(2) and P(3) elements were crucial to enhancing inhibitory activity. Although not optimized, a selected inhibitor was effective in attenuating type I collagen hydrolysis in a surrogate assay of bone resorption.
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Affiliation(s)
- John G Catalano
- Department of Medicinal Chemistry, GlaxoSmithKline, Research Triangle Park, NC 27709, USA
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39
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Fonovic M, Brömme D, Turk V, Turk B. Human cathepsin F: expression in baculovirus system, characterization and inhibition by protein inhibitors. Biol Chem 2004; 385:505-9. [PMID: 15255182 DOI: 10.1515/bc.2004.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Recombinant full-length human procathepsin F, produced in the baculovirus expression system, was partially processed during the purification procedure to a form lacking the N-terminal cystatin-like domain and activated with pepsin. Active cathepsin F efficiently hydrolyzed Z-FR-MCA (kcat/Km=106 mM(-1) s(-1)) and Bz-FVR-MCA (kcat/Km=8 mM(-1) s(-1)), whereas hydrolysis of Z-RR-MCA was very slow (kcat/Km<0.2 mM(-1) s(-1)). Cathepsin F was rapidly and tightly inhibited by cystatin C, chicken cystatin and equistatin with Ki values in the subnanomolar range (0.03-0.47 nM), whereas L-kininogen was a less strong inhibitor of the enzyme (Ki=4.7 nM). Stefin A inhibited cathepsin F slowly (kass=1.6 x 10(5) M(-1) s(-1)) and with a lower affinity (Ki=25 nM). These data suggest that cathepsin F differs from other related endopeptidases by considerably weaker inhibition by stefins.
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Affiliation(s)
- Marko Fonovic
- Department of Biochemistry and Molecular Biology, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
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40
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Deaton DN, Kumar S. Cathepsin K Inhibitors: Their Potential as Anti-Osteoporosis Agents. PROGRESS IN MEDICINAL CHEMISTRY 2004; 42:245-375. [PMID: 15003723 DOI: 10.1016/s0079-6468(04)42006-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Affiliation(s)
- David N Deaton
- Medicinal Chemistry Department, GlaxoSmithKline Inc., 5 Moore Drive, Research Triangle Park, NC 27709, USA
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41
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Tendulkar AV, Wangikar PP, Sohoni MA, Samant VV, Mone CY. Parameterization and Classification of the Protein Universe via Geometric Techniques. J Mol Biol 2003; 334:157-72. [PMID: 14596807 DOI: 10.1016/j.jmb.2003.09.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a scheme for the classification of 3487 non-redundant protein structures into 1207 non-hierarchical clusters by using recurring structural patterns of three to six amino acids as keys of classification. This results in several signature patterns, which seem to decide membership of a protein in a functional category. The patterns provide clues to the key residues involved in functional sites as well as in protein-protein interaction. The discovered patterns include a "glutamate double bridge" of superoxide dismutase, the functional interface of the serine protease and inhibitor, interface of homo/hetero dimers, and functional sites of several enzyme families. We use geometric invariants to decide superimposability of structural patterns. This allows the parameterization of patterns and discovery of recurring patterns via clustering. The geometric invariant-based approach eliminates the computationally explosive step of pair-wise comparison of structures. The results provide a vast resource for the biologists for experimental validation of the proposed functional sites, and for the design of synthetic enzymes, inhibitors and drugs.
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Affiliation(s)
- Ashish V Tendulkar
- Kanwal Rekhi School of Information Technology, Indian Institute of Technology, Bombay, Powai, Mumbai 400 076, India
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42
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Connolly KM, Smith BT, Pilpa R, Ilangovan U, Jung ME, Clubb RT. Sortase from Staphylococcus aureus does not contain a thiolate-imidazolium ion pair in its active site. J Biol Chem 2003; 278:34061-5. [PMID: 12824164 DOI: 10.1074/jbc.m305245200] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Many surface proteins are anchored to the cell wall by the action of sortase enzymes, a recently discovered family of cysteine transpeptidases. As the surface proteins of human pathogens are frequently required for virulence, the sortase-mediated anchoring reaction represents a potential target for new anti-infective agents. It has been suggested that the sortase from Staphylococcus aureus (SrtA), may use a similar catalytic strategy as the papain cysteine proteases, holding its Cys184 side chain in an active configuration through a thiolate-imidazolium ion interaction with residue His120. To investigate the mechanism of transpeptidation, we have synthesized a peptidyl-vinyl sulfone substrate mimic that irreversibly inhibits SrtA. Through the study of the pH dependence of SrtA inhibition and NMR, we have estimated the pKas of the active site thiol (Cys184) and imidazole (His120) to be approximately 9.4 and 7.0, respectively. These measurements are inconsistent with the existence of a thiolate-imidazolium ion pair and suggest a general base catalysis mechanism during transpeptidation.
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Affiliation(s)
- Kevin M Connolly
- Department of Chemistry and Biochemistry, Molecular Biology Institute and UCLA-Department of Energy Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095-1570, USA
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43
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Giles NM, Watts AB, Giles GI, Fry FH, Littlechild JA, Jacob C. Metal and redox modulation of cysteine protein function. CHEMISTRY & BIOLOGY 2003; 10:677-93. [PMID: 12954327 DOI: 10.1016/s1074-5521(03)00174-1] [Citation(s) in RCA: 321] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In biological systems, the amino acid cysteine combines catalytic activity with an extensive redox chemistry and unique metal binding properties. The interdependency of these three aspects of the thiol group permits the redox regulation of proteins and metal binding, metal control of redox activity, and ligand control of metal-based enzyme catalysis. Cysteine proteins are therefore able to act as "redox switches," to sense concentrations of oxidative stressors and unbound zinc ions in the cytosol, to provide a "storage facility" for excess metal ions, to control the activity of metalloproteins, and to take part in important regulatory and signaling pathways. The diversity of cysteine's multiple roles in vivo is equally as fascinating as it is promising for future biochemical and pharmacological research.
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Affiliation(s)
- Niroshini M Giles
- School of Biological and Chemical Sciences, University of Exeter, Stocker Road, EX4 4QD, Exeter, United Kingdom
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44
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Powers JC, Asgian JL, Ekici OD, James KE. Irreversible inhibitors of serine, cysteine, and threonine proteases. Chem Rev 2002; 102:4639-750. [PMID: 12475205 DOI: 10.1021/cr010182v] [Citation(s) in RCA: 818] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- James C Powers
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA.
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