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Marciniak B, Kciuk M, Mujwar S, Sundaraj R, Bukowski K, Gruszka R. In Vitro and In Silico Investigation of BCI Anticancer Properties and Its Potential for Chemotherapy-Combined Treatments. Cancers (Basel) 2023; 15:4442. [PMID: 37760412 PMCID: PMC10526149 DOI: 10.3390/cancers15184442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/10/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND DUSP6 phosphatase serves as a negative regulator of MAPK kinases involved in numerous cellular processes. BCI has been identified as a potential allosteric inhibitor with anticancer activity. Our study was designed to test the anticancer properties of BCI in colon cancer cells, to characterize the effect of this compound on chemotherapeutics such as irinotecan and oxaliplatin activity, and to identify potential molecular targets for this inhibitor. METHODS BCI cytotoxicity, proapoptotic activity, and cell cycle distribution were investigated in vitro on three colon cancer cell lines (DLD1, HT-29, and Caco-2). In silico investigation was prepared to assess BCI drug-likeness and identify potential molecular targets. RESULTS The exposure of colorectal cancer cells with BCI resulted in antitumor effects associated with cell cycle arrest and induction of apoptosis. BCI exhibited strong cytotoxicity on DLD1, HT-29, and Caco-2 cells. BCI showed no significant interaction with irinotecan, but strongly attenuated the anticancer activity of oxaliplatin when administered together. Analysis of synergy potential further confirmed the antagonistic interaction between these two compounds. In silico investigation indicated CDK5 as a potential new target of BCI. CONCLUSIONS Our studies point to the anticancer potential of BCI but note the need for a precise mechanism of action.
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Affiliation(s)
- Beata Marciniak
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland; (M.K.); (K.B.); (R.G.)
| | - Mateusz Kciuk
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland; (M.K.); (K.B.); (R.G.)
- Doctoral School of Exact and Natural Sciences, University of Lodz, 90-237 Lodz, Poland
| | - Somdutt Mujwar
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India;
| | - Rajamanikandan Sundaraj
- Centre for Drug Discovery, Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore 641021, Tamil Nadu, India;
| | - Karol Bukowski
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland; (M.K.); (K.B.); (R.G.)
| | - Renata Gruszka
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland; (M.K.); (K.B.); (R.G.)
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2
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Martins LS, Kruger HG, Naicker T, Alves CN, Lameira J, Araújo Silva JR. Computational insights for predicting the binding and selectivity of peptidomimetic plasmepsin IV inhibitors against cathepsin D. RSC Adv 2022; 13:602-614. [PMID: 36605626 PMCID: PMC9773328 DOI: 10.1039/d2ra06246a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Plasmepsins (Plms) are aspartic proteases involved in the degradation of human hemoglobin by P. falciparum and are essential for the survival and growth of the parasite. Therefore, Plm enzymes are reported as an important antimalarial drug target. Herein, we have applied molecular docking, molecular dynamics (MD) simulations, and binding free energy with the Linear Interaction Energy (LIE) approach to investigate the binding of peptidomimetic PlmIV inhibitors with a particular focus on understanding their selectivity against the human Asp protease cathepsin D (CatD). The residual decomposition analysis results suggest that amino acid differences in the subsite S3 of PlmIV and CatD are responsible for the higher selectivity of the 5a inhibitor. These findings yield excellent agreement with experimental binding data and provide new details regarding van der Waals and electrostatic interactions of subsite residues as well as structural properties of the PlmIV and CatD systems.
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Affiliation(s)
- Lucas Sousa Martins
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do ParáBelémPará 66075-110Brazil
| | | | - Tricia Naicker
- Catalysis and Peptide Research Unit, University of KwaZulu-NatalDurban 4000South Africa
| | - Cláudio Nahum Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do ParáBelémPará 66075-110Brazil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do ParáBelémPará 66075-110Brazil
| | - José Rogério Araújo Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do ParáBelémPará 66075-110Brazil
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3
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Bridging the Gap in Malaria Parasite Resistance, Current Interventions, and the Way Forward from in Silico Perspective: A Review. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227915. [PMID: 36432016 PMCID: PMC9692793 DOI: 10.3390/molecules27227915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/07/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022]
Abstract
The past decade has seen most antimalarial drugs lose their clinical potency stemming from parasite resistance. Despite immense efforts by researchers to mitigate this global scourge, a breakthrough is yet to be achieved, as most current malaria chemotherapies suffer the same fate. Though the etiology of parasite resistance is not well understood, the parasite's complex life has been implicated. A drug-combination therapy with artemisinin as the central drug, artemisinin-based combination therapy (ACT), is currently the preferred malaria chemotherapy in most endemic zones. The emerging concern of parasite resistance to artemisinin, however, has compromised this treatment paradigm. Membrane-bound Ca2+-transporting ATPase and endocytosis pathway protein, Kelch13, among others, are identified as drivers in plasmodium parasite resistance to artemisinin. To mitigate parasite resistance to current chemotherapy, computer-aided drug design (CADD) techniques have been employed in the discovery of novel drug targets and the development of small molecule inhibitors to provide an intriguing alternative for malaria treatment. The evolution of plasmepsins, a class of aspartyl acid proteases, has gained tremendous attention in drug discovery, especially the non-food vacuole. They are expressed at multi-stage of the parasite's life cycle and involve in hepatocytes' egress, invasion, and dissemination of the parasite within the human host, further highlighting their essentiality. In silico exploration of non-food vacuole plasmepsin, PMIX and PMX unearthed the dual enzymatic inhibitory mechanism of the WM382 and 49c, novel plasmepsin inhibitors presently spearheading the search for potent antimalarial. These inhibitors impose structural compactness on the protease, distorting the characteristic twist motion. Pharmacophore modeling and structure activity of these compounds led to the generation of hits with better affinity and inhibitory prowess towards PMIX and PMX. Despite these headways, the major obstacle in targeting PM is the structural homogeneity among its members and to human Cathepsin D. The incorporation of CADD techniques described in the study at early stages of drug discovery could help in selective inhibition to augment malaria chemotherapy.
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4
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Bunk J, Prieto Huarcaya S, Drobny A, Dobert JP, Walther L, Rose-John S, Arnold P, Zunke F. Corrigendum: Cathepsin D Variants Associated With Neurodegenerative Diseases Show Dysregulated Functionality and Modified α-Synuclein Degradation Properties. Front Cell Dev Biol 2021; 9:671532. [PMID: 34249927 PMCID: PMC8262674 DOI: 10.3389/fcell.2021.671532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/07/2021] [Indexed: 11/23/2022] Open
Affiliation(s)
- Josina Bunk
- Institute of Biochemistry, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Susy Prieto Huarcaya
- Institute of Biochemistry, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.,Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Alice Drobny
- Institute of Biochemistry, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.,Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jan Philipp Dobert
- Institute of Biochemistry, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.,Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Lina Walther
- Institute of Biochemistry, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Stefan Rose-John
- Institute of Biochemistry, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Philipp Arnold
- Institute of Anatomy, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.,Institute of Anatomy, Functional and Clinical Anatomy, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Friederike Zunke
- Institute of Biochemistry, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.,Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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5
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Cathepsin D-Managing the Delicate Balance. Pharmaceutics 2021; 13:pharmaceutics13060837. [PMID: 34198733 PMCID: PMC8229105 DOI: 10.3390/pharmaceutics13060837] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 12/11/2022] Open
Abstract
Lysosomal proteases play a crucial role in maintaining cell homeostasis. Human cathepsin D manages protein turnover degrading misfolded and aggregated proteins and favors apoptosis in the case of proteostasis disruption. However, when cathepsin D regulation is affected, it can contribute to numerous disorders. The down-regulation of human cathepsin D is associated with neurodegenerative disorders, such as neuronal ceroid lipofuscinosis. On the other hand, its excessive levels outside lysosomes and the cell membrane lead to tumor growth, migration, invasion and angiogenesis. Therefore, targeting cathepsin D could provide significant diagnostic benefits and new avenues of therapy. Herein, we provide a brief overview of cathepsin D structure, regulation, function, and its role in the progression of many diseases and the therapeutic potentialities of natural and synthetic inhibitors and activators of this protease.
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6
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Bunk J, Prieto Huarcaya S, Drobny A, Dobert JP, Walther L, Rose-John S, Arnold P, Zunke F. Cathepsin D Variants Associated With Neurodegenerative Diseases Show Dysregulated Functionality and Modified α-Synuclein Degradation Properties. Front Cell Dev Biol 2021; 9:581805. [PMID: 33681191 PMCID: PMC7928348 DOI: 10.3389/fcell.2021.581805] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
Cathepsin D (CTSD) is a lysosomal protease important for the degradation of various substrates, including disease-associated proteins like α-synuclein (a-syn), amyloid precursor protein (APP) and tau, all of which tend to aggregate if not efficiently degraded. Hence, it is not surprising that genetic variants within the CTSD gene have been linked to neurodegenerative diseases, like Parkinson’s and Alzheimer’s disease (PD, AD), as well as the lysosomal storage disorder neuronal ceroid lipofuscinosis type-10 (NCL10). Although recent studies have shown the molecular dependence of substrate degradation via CTSD within autophagic pathways, only little is known about the precise role of lysosomal CTSD function in disease development. We here performed biochemical, cellular and structural analyses of eleven disease-causing CTSD point mutations found in genomic sequencing data of patients to understand their role in neurodegeneration. These CTSD variants were analyzed for cellular localization, maturation and enzymatic activity in overexpression analyses. Moreover, for PD-associated mutants, intracellular degradation of a-syn was monitored. In summary, our results suggest that NCL10-associated CTSD variants are significantly impaired in lysosomal maturation and enzymatic activity, whereas the AD- and PD-associated variants seemed rather unaffected, indicating normal maturation, and lysosomal presence. Interestingly, a PD-associated CTSD variant (A239V) exhibited increased enzymatic activity accompanied by enhanced a-syn degradation. By structural analyses of this mutant utilizing molecular dynamics simulation (MDS), we identified a structural change within a loop adjacent to the catalytic center leading to a higher flexibility and potentially accelerated substrate exchange rates. Our data sheds light onto the role of CTSD in disease development and helps to understand the structural regulation of enzymatic function, which could be utilized for targeted CTSD activation. Because of the degradative function of CTSD, this enzyme is especially interesting for therapeutic strategies tackling protein aggregates in neurodegenerative disorders.
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Affiliation(s)
- Josina Bunk
- Institute of Biochemistry, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Susy Prieto Huarcaya
- Institute of Biochemistry, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.,Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Alice Drobny
- Institute of Biochemistry, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.,Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jan Philipp Dobert
- Institute of Biochemistry, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.,Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Lina Walther
- Institute of Biochemistry, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Stefan Rose-John
- Institute of Biochemistry, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Philipp Arnold
- Institute of Anatomy, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.,Institute of Anatomy, Functional and Clinical Anatomy, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Friederike Zunke
- Institute of Biochemistry, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.,Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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7
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Singh MP, Sharma C, Kang SC. Morin hydrate attenuates adenine-induced renal fibrosis via targeting cathepsin D signaling. Int Immunopharmacol 2020; 90:107234. [PMID: 33310295 DOI: 10.1016/j.intimp.2020.107234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 11/07/2020] [Accepted: 11/22/2020] [Indexed: 12/12/2022]
Abstract
Lysosomal proteases such as cathepsins B, D, L, and K can regulate the process of fibrosis in most of the organs. However, the role of cathepsin D (CATD) in kidney fibrosis and corresponding chronic kidney disease (CKD) is still unknown. We investigated whether CATD immunomodulation using morin hydrate (MH) can attenuate kidney fibrosis in CKD. Here, CKD was developed by an oral dosage of adenine (AD) in the mice model. Histopathological detection using H & E and Oil-Red-O staining revealed tissue deposition. An escalation in serum creatinine, albumin, and blood urea nitrogen (BUN) revealed a failure in kidney function. An increase in fibrosis was determined using protein analysis and mRNA analysis of MMP-9 and MMP-2 respectively. Both immunoblot analysis and histological analysis indicated that MH immunomudulated CATD expression in AD treated kidneys. With docking analysis, we found MH can bind with the catalytic core of CATD with binding efficiency of -6.83 kcal/mol. Further, MH prevented AD mediated fibrosis by reducing collagen fragmentation as evidenced by the decrease in MMP-2 (P < 0.05) and MMP-9 (P < 0.001) protein levels. MH lowered the levels of inflammation by reducing the AD enhanced expression of MCP-1 and COX-2 nearly threefold. MH treatment increased body weight, enhance kidney function, and improved survival by nearly 150% compared to AD treated mice. CATD inactivation by MH after AD treatment resulted in decreased ECM degradation, fibrosis, and inflammation which resulted in improved renal function and survival.
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Affiliation(s)
- Mahendra Pal Singh
- Department of Biotechnology, Daegu University, Gyeongsan, Gyeongbuk 38453, Republic of Korea; Department of Immunology, Mayo Clinic, Rochester MN55905, USA
| | - Chanchal Sharma
- Department of Biotechnology, Daegu University, Gyeongsan, Gyeongbuk 38453, Republic of Korea
| | - Sun Chul Kang
- Department of Biotechnology, Daegu University, Gyeongsan, Gyeongbuk 38453, Republic of Korea.
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8
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Goyal S, Patel KV, Nagare Y, Raykar DB, Raikar SS, Dolas A, Khurana P, Cyriac R, Sarak S, Gangar M, Agarwal AK, Kulkarni A. Identification and structure-activity relationship studies of small molecule inhibitors of the human cathepsin D. Bioorg Med Chem 2020; 29:115879. [PMID: 33271453 DOI: 10.1016/j.bmc.2020.115879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/08/2020] [Accepted: 11/13/2020] [Indexed: 01/18/2023]
Abstract
Cathepsin D, an aspartyl protease, is an attractive therapeutic target for various diseases, primarily cancer and osteoarthritis. However, despite several small molecule cathepsin D inhibitors being developed, that are highly potent, most of them show poor microsomal stability, which in turn limits their clinical translation. Herein, we describe the design, optimization and evaluation of a series of novel non-peptidic acylguanidine based small molecule inhibitors of cathepsin D. Optimization of our hit compound 1a (IC50 = 29 nM) led to the highly potent mono sulphonamide analogue 4b (IC50 = 4 nM), however with poor microsomal stability (HLM: 177 and MLM: 177 μl/min/mg). To further improve the microsomal stability while retaining the potency, we carried out an extensive structure-activity relationship screen which led to the identification of our optimised lead 24e (IC50 = 45 nM), with an improved microsomal stability (HLM: 59.1 and MLM: 86.8 μl/min/mg). Our efforts reveal that 24e could be a good starting point or potential candidate for further preclinical studies against diseases where Cathepsin D plays an important role.
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Affiliation(s)
| | | | - Yadav Nagare
- Aten Porus Lifesciences, Bangalore 560068, India
| | | | | | - Atul Dolas
- Aten Porus Lifesciences, Bangalore 560068, India
| | | | | | - Sharad Sarak
- Aten Porus Lifesciences, Bangalore 560068, India
| | | | - Anil K Agarwal
- Department of Chemistry, CHRIST (Deemed to be University), Bengaluru, Karnataka, India
| | - Aditya Kulkarni
- Aten Porus Lifesciences, Bangalore 560068, India; Avaliv Therapeutics, Naples, FL, USA.
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9
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Novel peptide ligands for antibody purification provide superior clearance of host cell protein impurities. J Chromatogr A 2020; 1625:461237. [DOI: 10.1016/j.chroma.2020.461237] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 05/10/2020] [Accepted: 05/12/2020] [Indexed: 11/19/2022]
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10
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Houštecká R, Hadzima M, Fanfrlík J, Brynda J, Pallová L, Hánová I, Mertlíková-Kaiserová H, Lepšík M, Horn M, Smrčina M, Majer P, Mareš M. Biomimetic Macrocyclic Inhibitors of Human Cathepsin D: Structure-Activity Relationship and Binding Mode Analysis. J Med Chem 2020; 63:1576-1596. [PMID: 32003991 DOI: 10.1021/acs.jmedchem.9b01351] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Human cathepsin D (CatD), a pepsin-family aspartic protease, plays an important role in tumor progression and metastasis. Here, we report the development of biomimetic inhibitors of CatD as novel tools for regulation of this therapeutic target. We designed a macrocyclic scaffold to mimic the spatial conformation of the minimal pseudo-dipeptide binding motif of pepstatin A, a microbial oligopeptide inhibitor, in the CatD active site. A library of more than 30 macrocyclic peptidomimetic inhibitors was employed for scaffold optimization, mapping of subsite interactions, and profiling of inhibitor selectivity. Furthermore, we solved high-resolution crystal structures of three macrocyclic inhibitors with low nanomolar or subnanomolar potency in complex with CatD and determined their binding mode using quantum chemical calculations. The study provides a new structural template and functional profile that can be exploited for design of potential chemotherapeutics that specifically inhibit CatD and related aspartic proteases.
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Affiliation(s)
- Radka Houštecká
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic.,First Faculty of Medicine , Charles University , Kateřinská 32 , 12108 Praha 2 , Czech Republic
| | - Martin Hadzima
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic.,Department of Organic Chemistry, Faculty of Science , Charles University , Albertov 6 , 12800 Praha 2 , Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic
| | - Lenka Pallová
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic
| | - Iva Hánová
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic.,Department of Biochemistry, Faculty of Science , Charles University , Albertov 6 , 12800 Praha 2 , Czech Republic
| | - Helena Mertlíková-Kaiserová
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic
| | - Martin Horn
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic
| | - Martin Smrčina
- Tucson Research Center , Icagen Inc. , 2090 E. Innovation Park Drive , Oro Valley , Arizona 85755 , United States
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic
| | - Michael Mareš
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic
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11
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Kang JM, Yoo WG, Lê HG, Thái TL, Hong SJ, Sohn WM, Na BK. Partial Characterization of Two Cathepsin D Family Aspartic Peptidases of Clonorchis sinensis. THE KOREAN JOURNAL OF PARASITOLOGY 2019; 57:671-680. [PMID: 31914521 PMCID: PMC6960241 DOI: 10.3347/kjp.2019.57.6.671] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 11/12/2019] [Indexed: 11/24/2022]
Abstract
Cathepsin D (CatD, EC 3.4.23.5) is a member belonging to the subfamily of aspartic endopeptidases, which are classified into the MEROPS clan AA, family A1. Helminth parasites express a large set of different peptidases that play pivotal roles in parasite biology and pathophysiology. However, CatD is less well known than the other classes of peptidases in terms of biochemical properties and biological functions. In this study, we identified 2 novel CatDs (CsCatD1 and CsCatD2) of Clonorchis sinensis and partially characterized their properties. Both CsCatDs represent typical enzymes sharing amino acid residues and motifs that are tightly conserved in the CatD superfamily of proteins. Both CsCatDs showed similar patterns of expression in different developmental stages of C. sinensis, but CsCatD2 was also expressed in metacercariae. CsCatD2 was mainly expressed in the intestines and eggs of C. sinensis. Sera obtained from rats experimentally infected with C. sinensis reacted with recombinant CsCatD2 beginning 2 weeks after infection and the antibody titers were gradually increased by maturation of the parasite. Structural analysis of CsCatD2 revealed a bilobed enzyme structure consisting of 2 antiparallel β-sheet domains packed against each other forming a homodimeric structure. These results suggested a plausible biological role of CsCatD2 in the nutrition and reproduction of parasite and its potential utility as a serodiagnostic antigen in clonorchiasis.
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Affiliation(s)
- Jung-Mi Kang
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727, Korea.,BK21Plus Team for Anti-aging Biotechnology and Industry, Department of Convergence Medical Science, Gyeongsang National University, Jinju 52727, Korea
| | - Won-Gi Yoo
- Department of Medical Environmental Biology, Chung-Ang University College of Medicine, Seoul 06974, Korea
| | - Hương Giang Lê
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727, Korea.,BK21Plus Team for Anti-aging Biotechnology and Industry, Department of Convergence Medical Science, Gyeongsang National University, Jinju 52727, Korea
| | - Thị Lam Thái
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727, Korea.,BK21Plus Team for Anti-aging Biotechnology and Industry, Department of Convergence Medical Science, Gyeongsang National University, Jinju 52727, Korea
| | - Sung-Jong Hong
- Department of Medical Environmental Biology, Chung-Ang University College of Medicine, Seoul 06974, Korea
| | - Woon-Mok Sohn
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727, Korea
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12
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Francisco CC, Luis CLJ, Marina EBJ, Javier CMF, Alexis LZA, Del Carmen SOH, Alfredo REI. Effect of Temperature and pH on the Secondary Structure and Denaturation Process of Jumbo Squid Hepatopancreas Cathepsin D. Protein Pept Lett 2019; 26:532-541. [PMID: 30950340 DOI: 10.2174/0929866526666190405124353] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND Cathepsin D is a lysosomal enzyme that is found in all organisms acting in protein turnover, in humans it is present in some types of carcinomas, and it has a high activity in Parkinson's disease and a low activity in Alzheimer disease. In marine organisms, most of the research has been limited to corroborate the presence of this enzyme. It is known that cathepsin D of some marine organisms has a low thermostability and that it has the ability to have activity at very acidic pH. Cathepsin D of the Jumbo squid (Dosidicus gigas) hepatopancreas was purified and partially characterized. The secondary structure of these enzymes is highly conserved so the role of temperature and pH in the secondary structure and in protein denaturation is of great importance in the study of enzymes. The secondary structure of cathepsin D from jumbo squid hepatopancreas was determined by means of circular dichroism spectroscopy. OBJECTIVE In this article, our purpose was to determine the secondary structure of the enzyme and how it is affected by subjecting it to different temperature and pH conditions. METHODS Circular dichroism technique was used to measure the modifications of the secondary structure of cathepsin D when subjected to different treatments. The methodology consisted in dissecting the hepatopancreas of squid and freeze drying it. Then a crude extract was prepared by mixing 1: 1 hepatopancreas with assay buffer, the purification was in two steps; the first step consisted of using an ultrafiltration membrane with a molecular cut of 50 kDa, and the second step, a pepstatin agarose resin was used to purification the enzyme. Once the enzyme was purified, the purity was corroborated with SDS PAGE electrophoresis, isoelectric point and zymogram. Circular dichroism is carried out by placing the sample with a concentration of 0.125 mg / mL in a 3 mL quartz cell. The results were obtained in mdeg (millidegrees) and transformed to mean ellipticity per residue, using 111 g/mol molecular weight/residue as average. Secondary-structure estimation from the far-UV CD spectra was calculated using K2D Dichroweb software. RESULTS It was found that α helix decreases at temperatures above 50 °C and above pH 4. Heating the enzyme above 70°C maintains a low percentage of α helix and increases β sheet. Far-UV CD measurements of cathepsin D showed irreversible thermal denaturation. The process was strongly dependent on the heating rate, accompanied by a process of oligomerization of the protein that appears when the sample is heated, and maintained a certain time at this temperature. An amount typically between 3 and 4% α helix of their secondary structure remains unchanged. It is consistent with an unfolding process kinetically controlled due to the presence of an irreversible reaction. The secondary structure depends on pH, and a pH above 4 causes α helix structures to be modified. CONCLUSION In conclusion, cathepsin D from jumbo squid hepatopancreas showed retaining up to 4% α helix at 80°C. The thermal denaturation of cathepsin D at pH 3.5 is under kinetic control and follows an irreversible model.
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Affiliation(s)
- Cadena-Cadena Francisco
- Departamento de Investigacion y Posgrado de Alimentos, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Cárdenas-López José Luis
- Departamento de Investigacion y Posgrado de Alimentos, Universidad de Sonora, Hermosillo, Sonora, Mexico
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Gilles P, Wenck K, Stratmann I, Kirsch M, Smolin DA, Schaller T, de Groot H, Kraft A, Schrader T. High-Affinity Copolymers Inhibit Digestive Enzymes by Surface Recognition. Biomacromolecules 2017; 18:1772-1784. [DOI: 10.1021/acs.biomac.7b00162] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Arno Kraft
- Heriot-Watt University, Edinburgh, Scotland, United Kingdom EH14 4AS
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14
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Hernández-Rodríguez M, Correa-Basurto J, Gutiérrez A, Vitorica J, Rosales-Hernández MC. Asp32 and Asp228 determine the selective inhibition of BACE1 as shown by docking and molecular dynamics simulations. Eur J Med Chem 2016; 124:1142-1154. [DOI: 10.1016/j.ejmech.2016.08.028] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 08/10/2016] [Accepted: 08/13/2016] [Indexed: 11/28/2022]
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15
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Czodrowski P, Mallinger A, Wienke D, Esdar C, Pöschke O, Busch M, Rohdich F, Eccles SA, Ortiz-Ruiz MJ, Schneider R, Raynaud FI, Clarke PA, Musil D, Schwarz D, Dale T, Urbahns K, Blagg J, Schiemann K. Structure-Based Optimization of Potent, Selective, and Orally Bioavailable CDK8 Inhibitors Discovered by High-Throughput Screening. J Med Chem 2016; 59:9337-9349. [PMID: 27490956 DOI: 10.1021/acs.jmedchem.6b00597] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The mediator complex-associated cyclin dependent kinase CDK8 regulates β-catenin-dependent transcription following activation of WNT signaling. Multiple lines of evidence suggest CDK8 may act as an oncogene in the development of colorectal cancer. Here we describe the successful optimization of an imidazo-thiadiazole series of CDK8 inhibitors that was identified in a high-throughput screening campaign and further progressed by structure-based design. In several optimization cycles, we improved the microsomal stability, potency, and kinase selectivity. The initial imidazo-thiadiazole scaffold was replaced by a 3-methyl-1H-pyrazolo[3,4-b]-pyridine which resulted in compound 25 (MSC2530818) that displayed excellent kinase selectivity, biochemical and cellular potency, microsomal stability, and is orally bioavailable. Furthermore, we demonstrated modulation of phospho-STAT1, a pharmacodynamic biomarker of CDK8 activity, and tumor growth inhibition in an APC mutant SW620 human colorectal carcinoma xenograft model after oral administration. Compound 25 demonstrated suitable potency and selectivity to progress into preclinical in vivo efficacy and safety studies.
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Affiliation(s)
- Paul Czodrowski
- Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany
| | - Aurélie Mallinger
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research , London, SW7 3RP, U.K
| | - Dirk Wienke
- Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany
| | - Christina Esdar
- Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany
| | - Oliver Pöschke
- Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany
| | - Michael Busch
- Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany
| | - Felix Rohdich
- Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany
| | - Suzanne A Eccles
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research , London, SW7 3RP, U.K
| | - Maria-Jesus Ortiz-Ruiz
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research , London, SW7 3RP, U.K
| | | | - Florence I Raynaud
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research , London, SW7 3RP, U.K
| | - Paul A Clarke
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research , London, SW7 3RP, U.K
| | - Djordje Musil
- Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany
| | - Daniel Schwarz
- Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany
| | - Trevor Dale
- School of Bioscience, Cardiff University , Cardiff, CF10 3AX, U.K
| | - Klaus Urbahns
- Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research , London, SW7 3RP, U.K
| | - Kai Schiemann
- Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany
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Anantaraju HS, Battu MB, Viswanadha S, Sriram D, Yogeeswari P. Cathepsin D inhibitors as potential therapeutics for breast cancer treatment: Molecular docking and bioevaluation against triple-negative and triple-positive breast cancers. Mol Divers 2015; 20:521-35. [PMID: 26563150 DOI: 10.1007/s11030-015-9645-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/24/2015] [Indexed: 10/22/2022]
Abstract
The main aim of this study was to discover small molecule inhibitors against Cathepsin D (CatD) (EC.3.4.23.5), a clinically proven prognostic marker for breast cancer, and to explore the mechanisms by which CatD could be a useful therapeutic target for triple-positive and triple-negative breast cancers (TPBC & TNBC). The crystal structure of CatD at 2.5 Å resolution (PDB: 1LYB), which was complexed with Pepstatin A, was selected for computer-aided molecular modeling. The methods used in our study were pharmacophore modeling and molecular docking. Virtual screening was performed to identify small molecules from an in-house database and a large commercial chemical library. Cytotoxicity studies were performed on human normal cell line HEK293T and growth inhibition studies on breast adenocarcinoma cell lines, namely MCF-7, MDA-MB-231, SK-BR-3, and MDA-MB-468. Furthermore, RT-PCR analysis, in vitro enzyme assay, and cell cycle analysis ascertained the validity of the selected molecules. A set of 28 molecules was subjected to an in vitro fluorescence-based inhibitory activity assay, and among them six molecules exhibited >50 % inhibition at 25μM. These molecules also exhibited good growth inhibition against TPBC and TNBC cancer types. Among them, molecules 1 and 17 showed single-digit micromolar GI50 values against MCF-7 and MDA-MB-231 cell lines.
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Affiliation(s)
- Hasitha Shilpa Anantaraju
- Computer-Aided Drug Design Laboratory, Department of Pharmacy, Birla Institute of Technology & Science- Pilani, Hyderabad Campus, Shameerpet, R.R. District, Hyderabad, 500078, Telangana, India
| | - Madhu Babu Battu
- Computer-Aided Drug Design Laboratory, Department of Pharmacy, Birla Institute of Technology & Science- Pilani, Hyderabad Campus, Shameerpet, R.R. District, Hyderabad, 500078, Telangana, India
| | - Srikant Viswanadha
- Incozen Therapeutics (P)Ltd, Shameerpet, R.R. District, Hyderabad, 500078, Telangana, India
| | - Dharmarajan Sriram
- Computer-Aided Drug Design Laboratory, Department of Pharmacy, Birla Institute of Technology & Science- Pilani, Hyderabad Campus, Shameerpet, R.R. District, Hyderabad, 500078, Telangana, India.,Yogee'S Bioinnovations Private Limited, Room No. 5, Technology Business Incubator, Birla Institute of Technology & Science- Pilani, Hyderabad Campus, Shameerpet, Hyderabad, 500078, Telangana, India
| | - Perumal Yogeeswari
- Computer-Aided Drug Design Laboratory, Department of Pharmacy, Birla Institute of Technology & Science- Pilani, Hyderabad Campus, Shameerpet, R.R. District, Hyderabad, 500078, Telangana, India. .,Yogee'S Bioinnovations Private Limited, Room No. 5, Technology Business Incubator, Birla Institute of Technology & Science- Pilani, Hyderabad Campus, Shameerpet, Hyderabad, 500078, Telangana, India.
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