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Dakilah I, Harb A, Abu-Gharbieh E, El-Huneidi W, Taneera J, Hamoudi R, Semreen MH, Bustanji Y. Potential of CDC25 phosphatases in cancer research and treatment: key to precision medicine. Front Pharmacol 2024; 15:1324001. [PMID: 38313315 PMCID: PMC10834672 DOI: 10.3389/fphar.2024.1324001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/04/2024] [Indexed: 02/06/2024] Open
Abstract
The global burden of cancer continues to rise, underscoring the urgency of developing more effective and precisely targeted therapies. This comprehensive review explores the confluence of precision medicine and CDC25 phosphatases in the context of cancer research. Precision medicine, alternatively referred to as customized medicine, aims to customize medical interventions by taking into account the genetic, genomic, and epigenetic characteristics of individual patients. The identification of particular genetic and molecular drivers driving cancer helps both diagnostic accuracy and treatment selection. Precision medicine utilizes sophisticated technology such as genome sequencing and bioinformatics to elucidate genetic differences that underlie the proliferation of cancer cells, hence facilitating the development of customized therapeutic interventions. CDC25 phosphatases, which play a crucial role in governing the progression of the cell cycle, have garnered significant attention as potential targets for cancer treatment. The dysregulation of CDC25 is a characteristic feature observed in various types of malignancies, hence classifying them as proto-oncogenes. The proteins in question, which operate as phosphatases, play a role in the activation of Cyclin-dependent kinases (CDKs), so promoting the advancement of the cell cycle. CDC25 inhibitors demonstrate potential as therapeutic drugs for cancer treatment by specifically blocking the activity of CDKs and modulating the cell cycle in malignant cells. In brief, precision medicine presents a potentially fruitful option for augmenting cancer research, diagnosis, and treatment, with an emphasis on individualized care predicated upon patients' genetic and molecular profiles. The review highlights the significance of CDC25 phosphatases in the advancement of cancer and identifies them as promising candidates for therapeutic intervention. This statement underscores the significance of doing thorough molecular profiling in order to uncover the complex molecular characteristics of cancer cells.
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Affiliation(s)
- Ibraheem Dakilah
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Amani Harb
- Department of Basic Sciences, Faculty of Arts and Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Eman Abu-Gharbieh
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Waseem El-Huneidi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Jalal Taneera
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Rifat Hamoudi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Division of Surgery and Interventional Science, University College London, London, United Kingdom
| | - Mohammed H Semreen
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | - Yasser Bustanji
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- School of Pharmacy, The University of Jordan, Amman, Jordan
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2
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Li LP, Li HX, Zhou H, Li WY, Wang RL, Zhang YC, Ma Y. Exploring the mechanism of C473D mutation on CDC25B causing weak binding affinity with CDK2/CyclinA by molecular dynamics study. J Biomol Struct Dyn 2023; 41:12552-12564. [PMID: 36655391 DOI: 10.1080/07391102.2023.2166995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 01/05/2023] [Indexed: 01/20/2023]
Abstract
CDC25B belongs to the CDC25 family, and it plays an important part in regulating the activity of CDK/CyclinA. Studies have shown that CDC25B is closely related to cancer development. When CYS473 on CDC25B is mutated into ASP, the affinity between CDC25B and CDK2/CyclinA weakens, and their dissociation speed is greatly improved. However, the mechanism by which the CDC25BC473D mutant weakens its binding to CDK2/CyclinA is unclear. In order to study the effect of CDC25BC473D mutants on CDK2/CyclinA substrates, we constructed and verified the rationality of the CDC25BWT:CDK2/CyclinA system and CDC25BC473D:CDK2/CyclinA system and conducted molecular dynamics (MD) simulation analysis. In the post-analysis, the fluctuations of residues ARG488-SER499, LYS541-TRP550 on CDC25B and residues ASP206-ASP210 on CDK2 were massive in the mutant CDC25BC473D:CDK2/CyclinA system. And the interactions between residue ARG492 and residue GLU208, residue ARG544 and residue GLU42, residue ARG544 and TRP550 were weakened in the mutant CDC25BC473D:CDK2/CyclinA system. The results showed that when CYS473 on CDC25B was mutated into ASP473, the mutant CDC25BC473D:CDK2/CyclinA system was less stable than the wild-type CDC25BWT:CDK2/CyclinA system. Finally, active site CYS473 of CDC25B was speculated to be the key residue, which had great effects on the binding between CDC25BCYS473 and CDK2 in the CDC25BC473D:CDK2/CyclinA system. Consequently, overall analyses appeared in this study ultimately provided a useful understanding of the weak interactions between CDC25BCYS473D and CDK2/CyclinA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Li-Peng Li
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
| | - Hao-Xin Li
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
| | - Hui Zhou
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
| | - Wei-Ya Li
- China Department of Pharmacy, Tianjin Medical University, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Run-Ling Wang
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
| | - Ying-Chi Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Ying Ma
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, People's Republic of China
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Faria AVS, Fonseca EMB, Fernandes-Oliveira PDS, de Lima TI, Clerici SP, Justo GZ, Silveira LR, Durán N, Ferreira-Halder CV. Violacein switches off low molecular weight tyrosine phosphatase and rewires mitochondria in colorectal cancer cells. Bioorg Chem 2022; 127:106000. [PMID: 35853296 DOI: 10.1016/j.bioorg.2022.106000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/26/2022]
Abstract
In the last decade, emerging evidence has shown that low molecular weight protein tyrosine phosphatase (LMWPTP) not only contributes to the progression of cancer but is associated with prostate low survival rate and colorectal cancer metastasis. We report that LMWPTP favors the glycolytic profile in some tumors. Therefore, the focus of the present study was to identify metabolic enzymes that correlate with LMWPTP expression in patient samples. Exploratory data analysis from RNA-seq, proteomics, and histology staining, confirmed the higher expression of LMWPTP in CRC. Our descriptive statistical analyses indicate a positive expression correlation between LMWPTP and energy metabolism enzymes such as acetyl-CoA carboxylase (ACC) and fatty acid synthase (FASN). In addition, we examine the potential of violacein to reprogram energetic metabolism and LMWPTP activity. Violacein treatment induced a shift of glycolytic to oxidative metabolism associated with alteration in mitochondrial efficiency, as indicated by higher oxygen consumption rate. Particularly, violacein treated cells displayed higher proton leak and ATP-linked oxygen consumption rate (OCR) as an indicator of the OXPHOS preference. Notably, violacein is able to bind and inhibit LMWPTP. Since the LMWPTP acts as a hub of signaling pathways that offer tumor cells invasive advantages, such as survival and the ability to migrate, our findings highlight an unexplored potential of violacein in circumventing the metabolic plasticity of tumor cells.
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Affiliation(s)
- Alessandra V S Faria
- Department of Biochemistry and Tissue Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Emanuella M B Fonseca
- Department of Biochemistry and Tissue Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil; Federal Institute of Education, Science and Technology of São Paulo (IFSP), São Roque, São Paulo, Brazil
| | | | - Tanes I de Lima
- Department of Structural and Functional Biology, University of Campinas, (UNICAMP), Campinas, SP, Brazil
| | - Stefano P Clerici
- Department of Biochemistry and Tissue Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Giselle Z Justo
- Department of Pharmaceutical Sciences and Department of Biochemistry, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Leonardo R Silveira
- Department of Structural and Functional Biology, University of Campinas, (UNICAMP), Campinas, SP, Brazil
| | - Nelson Durán
- Laboratory of Urogenital Carcinogenesis and Immunotherapy, Department of Structural and Functional Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil; Nanomedicine Research Unit (Nanomed), Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), Santo André, Brazil
| | - Carmen V Ferreira-Halder
- Department of Biochemistry and Tissue Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil.
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Passo MDS, Carvalho GGCD. In silico evaluation of potential drugs for the treatment of Colorectal Carcinoma. BRAZ J PHARM SCI 2022. [DOI: 10.1590/s2175-97902022e20343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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Li HX, Yang WY, Li LP, Zhou H, Li WY, Ma Y, Wang RL. Molecular dynamics study of CDC25B R492L mutant causing the activity decrease of CDC25B. J Mol Graph Model 2021; 109:108030. [PMID: 34509094 DOI: 10.1016/j.jmgm.2021.108030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/01/2021] [Accepted: 09/05/2021] [Indexed: 11/25/2022]
Abstract
Cell division cycle 25B (CDC25B) was responsible for regulating the various stages of cell division in the cell cycle. R492L was one of the common types of CDC25B mutants. Researches showed that compared to CDC25BWT, CDC25BR492L mutant had a ∼100-fold reduction in the rate constant for forming phosphatase intermediate (k2). However, the molecular basis of how the CDC25BR492L mutant influenced the process of binding between CDC25B and CDK2/CyclinA was not yet known. Therefore, the optimizations of three-dimensional structure of the CDC25BWT-CDK2/CyclinA system and the CDC25BR492L-CDK2/CyclinA system were constructed by ZDOCK and RDOCK, and five methods were employed to verify the reasonability of the docking structure. Then the molecular dynamics simulations on the two systems were performed to explore the reason why CDC25BR492L mutant caused the weak interactions between CDC25BR492L and CDK2/CyclinA, respectively. The remote docking site (Arg488-Tyr497) and the second active site (Lys538-Arg544) of CDC25B were observed to have high fluctuations in the CDC25BR492L-CDK2/CyclinA system with post-analysis, where the high fluctuation of these two regions resulted in weak interactions between CD25B and CDK2. In addition, Asp38-Glu42 and Asp206-Asp210 of CDK2 showed the slightly descending fluctuation, and CDK2 revealed an enhanced the self-interaction, which made CDK2 keep a relatively stable state in the CDC25BR492L-CDK2/CyclinA system. Finally, Leu492 of CDC25B was speculated to be the key residue, which had great effects on the binding between CDC25BR492L and CDK2 in the CDC25BR492L-CDK2/CyclinA system. Consequently, overall analyses appeared in this study ultimately offered a helpful understanding of the weak interactions between CDC25BR492L and CDK2.
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Affiliation(s)
- Hao-Xin Li
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Wen-Yu Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, People's Republic of China
| | - Li-Peng Li
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Hui Zhou
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Wei-Ya Li
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Ying Ma
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, People's Republic of China.
| | - Run-Ling Wang
- Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, People's Republic of China.
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Design, synthesis, and functional evaluation of triazine-based bivalent agents that simultaneously target the active site and hot spot of phosphatase Cdc25B. Bioorg Med Chem Lett 2021; 48:128265. [PMID: 34273487 DOI: 10.1016/j.bmcl.2021.128265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/05/2021] [Accepted: 07/11/2021] [Indexed: 11/21/2022]
Abstract
Cdc25B phosphatase catalyzes the dephosphorylation and activation of cyclin-dependent kinases 2 (CDK2/CycA) and their overexpression has been reported in cancers. Although Cdc25B has received much attention as a drug target, its flat and featureless surface makes it challenging to develop new agents targeting this protein. In this study, we investigated the rational design of a series of bivalent triazine-based derivatives with the aim of simultaneously targeting the active site and the remote hotspot critical for the interaction with CDK2/CycA. Compounds 1e and 10, containing aromatic residues, were shown to inhibit Cdc25B activity selectively over Cdc25A at low micromolar concentration.
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In Silico Identification of Small Molecules as New Cdc25 Inhibitors through the Correlation between Chemosensitivity and Protein Expression Pattern. Int J Mol Sci 2021; 22:ijms22073714. [PMID: 33918281 PMCID: PMC8038176 DOI: 10.3390/ijms22073714] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 01/11/2023] Open
Abstract
The cell division cycle 25 (Cdc25) protein family plays a crucial role in controlling cell proliferation, making it an excellent target for cancer therapy. In this work, a set of small molecules were identified as Cdc25 modulators by applying a mixed ligand-structure-based approach and taking advantage of the correlation between the chemosensitivity of selected structures and the protein expression pattern of the proposed target. In the first step of the in silico protocol, a set of molecules acting as Cdc25 inhibitors were identified through a new ligand-based protocol and the evaluation of a large database of molecular structures. Subsequently, induced-fit docking (IFD) studies allowed us to further reduce the number of compounds biologically screened. In vitro antiproliferative and enzymatic inhibition assays on the selected compounds led to the identification of new structurally heterogeneous inhibitors of Cdc25 proteins. Among them, J3955, the most active inhibitor, showed concentration-dependent antiproliferative activity against HepG2 cells, with GI50 in the low micromolar range. When J3955 was tested in cell-cycle perturbation experiments, it caused mitotic failure by G2/M-phase cell-cycle arrest. Finally, Western blotting analysis showed an increment of phosphorylated Cdk1 levels in cells exposed to J3955, indicating its specific influence in cellular pathways involving Cdc25 proteins.
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Tao Y, Hao X, Ding X, Cherukupalli S, Song Y, Liu X, Zhan P. Medicinal chemistry insights into novel CDC25 inhibitors. Eur J Med Chem 2020; 201:112374. [PMID: 32603979 DOI: 10.1016/j.ejmech.2020.112374] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/18/2022]
Abstract
Cell division cycle 25 (CDC25) phosphatases, a kind of cell cycle regulators, have become an attractive target for drug discovery, as they have been found to be over-expressed in various human cancer cells. Several CDC25 inhibitors have achieved significant attention in clinical trials with possible mechanistic actions. Prompted by the significance of CDC25 inhibitors with medicinal chemistry prospect, it is an apt time to review the various drug discovery methods involved in CDC25 drug discovery including high throughput screening (HTS), virtual screening (VS), fragment-based drug design, substitution decorating approach, structural simplification approach and scaffold hopping method to seek trends and identify promising new avenues of CDC25 drug discovery.
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Affiliation(s)
- Yucen Tao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Xia Hao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Xiao Ding
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Srinivasulu Cherukupalli
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Yuning Song
- Department of Clinical Pharmacy, Qilu Hospital of Shandong University, 250012, Jinan, China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China.
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Jing L, Wu G, Hao X, Olotu FA, Kang D, Chen CH, Lee KH, Soliman ME, Liu X, Song Y, Zhan P. Identification of highly potent and selective Cdc25 protein phosphatases inhibitors from miniaturization click-chemistry-based combinatorial libraries. Eur J Med Chem 2019; 183:111696. [DOI: 10.1016/j.ejmech.2019.111696] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/03/2019] [Accepted: 09/11/2019] [Indexed: 01/23/2023]
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Thornton BP, Johns A, Al-Shidhani R, Álvarez-Carretero S, Storer ISR, Bromley MJ, Tabernero L. Identification of Functional and Druggable Sites in Aspergillus fumigatus Essential Phosphatases by Virtual Screening. Int J Mol Sci 2019; 20:ijms20184636. [PMID: 31546755 PMCID: PMC6769645 DOI: 10.3390/ijms20184636] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/13/2019] [Accepted: 09/15/2019] [Indexed: 12/17/2022] Open
Abstract
Fungal diseases are a serious health burden worldwide with drug resistance compromising efficacy of the limited arsenal of antifungals available. New drugs with novel mechanisms of action are desperately needed to overcome current challenges. The screening of the Aspergillus fumigatus genome identified 35 phosphatases, four of which were previously reported as essential for viability. In addition, we validated another three essential phosphatases. Phosphatases control critical events in fungi from cell wall integrity to cell cycle, thus they are attractive targets for drug development. We used VSpipe v1.0, a virtual screening pipeline, to evaluate the druggability of the seven essential phosphatases and identify starting points for drug discovery. Targeted virtual screening and evaluation of the ligand efficiency plots created by VSpipe, enabled us to define the most favourable chemical space for drug development and suggested different modes of inhibition for each phosphatase. Interestingly, the identified ligand binding sites match with functional sites (active site and protein interaction sites) reported for other yeast and human homologues. Thus, the VSpipe virtual screening approach identified both druggable and functional sites in these essential phosphatases for further experimental validation and antifungal drug development.
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Affiliation(s)
- Benjamin P Thornton
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Anna Johns
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Reem Al-Shidhani
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Sandra Álvarez-Carretero
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Isabelle S R Storer
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Michael J Bromley
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK
| | - Lydia Tabernero
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UK.
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Al-Nour MY, Ibrahim MM, Elsaman T. Ellagic Acid, Kaempferol, and Quercetin from Acacia nilotica: Promising Combined Drug With Multiple Mechanisms of Action. ACTA ACUST UNITED AC 2019; 5:255-280. [PMID: 32226726 PMCID: PMC7100491 DOI: 10.1007/s40495-019-00181-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The pharmacological activity of Acacia nilotica's phytochemical constituents was confirmed with evidence-based studies, but the determination of exact targets that they bind and the mechanism of action were not done; consequently, we aim to identify the exact targets that are responsible for the pharmacological activity via the computational methods. Furthermore, we aim to predict the pharmacokinetics (ADME) properties and the safety profile in order to identify the best drug candidates. To achieve those goals, various computational methods were used including the ligand-based virtual screening and molecular docking. Moreover, pkCSM and SwissADME web servers were used for the prediction of pharmacokinetics and safety. The total number of the investigated compounds and targets was 25 and 61, respectively. According to the results, the pharmacological activity was attributed to the interaction with essential targets. Ellagic acid, Kaempferol, and Quercetin were the best A. nilotica's phytochemical constituents that contribute to the therapeutic activities, were non-toxic as well as non-carcinogen. The administration of Ellagic acid, Kaempferol, and Quercetin as combined drug via the novel drug delivery systems will be a valuable therapeutic choice for the treatment of recent diseases attacking the public health including cancer, multidrug-resistant bacterial infections, diabetes mellitus, and chronic inflammatory systemic disease.
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Affiliation(s)
- Mosab Yahya Al-Nour
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Omdurman Islamic University, Omdurman, Sudan
| | - Musab Mohamed Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Omdurman Islamic University, Omdurman, Sudan
| | - Tilal Elsaman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Omdurman Islamic University, Omdurman, Sudan
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Al-Hrout A, Chaiboonchoe A, Khraiwesh B, Murali C, Baig B, El-Awady R, Tarazi H, Alzahmi A, Nelson DR, Greish YE, Ramadan W, Salehi-Ashtiani K, Amin A. Safranal induces DNA double-strand breakage and ER-stress-mediated cell death in hepatocellular carcinoma cells. Sci Rep 2018; 8:16951. [PMID: 30446676 PMCID: PMC6240095 DOI: 10.1038/s41598-018-34855-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 10/26/2018] [Indexed: 12/21/2022] Open
Abstract
Poor prognoses remain the most challenging aspect of hepatocellular carcinoma (HCC) therapy. Consequently, alternative therapeutics are essential to control HCC. This study investigated the anticancer effects of safranal against HCC using in vitro, in silico, and network analyses. Cell cycle and immunoblot analyses of key regulators of cell cycle, DNA damage repair and apoptosis demonstrated unique safranal-mediated cell cycle arrest at G2/M phase at 6 and 12 h, and at S-phase at 24 h, and a pronounced effect on DNA damage machinery. Safranal also showed pro-apoptotic effect through activation of both intrinsic and extrinsic initiator caspases; indicating ER stress-mediated apoptosis. Gene set enrichment analysis provided consistent findings where UPR is among the top terms of up-regulated genes in response to safranal treatment. Thus, proteins involved in ER stress were regulated through safranal treatment to induce UPR in HepG2 cells.
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Affiliation(s)
- Ala'a Al-Hrout
- Biology Department, College of Science, UAE University, P.O. Box 15551, Al-Ain, UAE
| | - Amphun Chaiboonchoe
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, UAE
| | - Basel Khraiwesh
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, UAE
- Center for Genomics and Systems Biology (CGSB), Division of Science, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, UAE
| | - Chandraprabha Murali
- Biology Department, College of Science, UAE University, P.O. Box 15551, Al-Ain, UAE
| | - Badriya Baig
- Biology Department, College of Science, UAE University, P.O. Box 15551, Al-Ain, UAE
| | - Raafat El-Awady
- College of Pharmacy and Sharjah Institute for Medical Research, University of Sharjah, Sharjah, UAE
| | - Hamadeh Tarazi
- College of Pharmacy and Sharjah Institute for Medical Research, University of Sharjah, Sharjah, UAE
| | - Amnah Alzahmi
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, UAE
| | - David R Nelson
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, UAE
| | | | - Wafaa Ramadan
- College of Pharmacy and Sharjah Institute for Medical Research, University of Sharjah, Sharjah, UAE
| | - Kourosh Salehi-Ashtiani
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, UAE.
- Center for Genomics and Systems Biology (CGSB), Division of Science, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, UAE.
| | - Amr Amin
- Biology Department, College of Science, UAE University, P.O. Box 15551, Al-Ain, UAE.
- Zoology Department, Cairo University, Giza, Egypt.
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13
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Zhang S, Jia Q, Gao Q, Fan X, Weng Y, Su Z. Dual-Specificity Phosphatase CDC25B Was Inhibited by Natural Product HB-21 Through Covalently Binding to the Active Site. Front Chem 2018; 6:531. [PMID: 30555816 PMCID: PMC6282036 DOI: 10.3389/fchem.2018.00531] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 10/12/2018] [Indexed: 12/14/2022] Open
Abstract
Cysteine 473, within the active site of the enzyme, Cdc25B, is catalytically essential for substrate activation. The most well-reported inhibitors of Cdc25 phosphatases, especially quinone-type inhibitors, function by inducing irreversible oxidation at this active site of cysteine. Here, we identified a natural product, HB-21, having a sesquiterpene lactone skeleton that could irreversibly bind to cys473 through the formation of a covalent bond. This compound inhibited recombinant human Cdc25B phosphatase with an IC50 value of 24.25 μM. Molecular modeling predicted that HB-21 not only covalently binds to cys473 of Cdc25B but also forms six hydrogen bonds with residues at the active site. Moreover, HB-21 can dephosphorylate cyclin-dependent kinase (CDK1), the natural substrate of Cdc25b, and inhibit cell cycle progression. In summary, HB-21 is a new type of Cdc25B inhibitor with a novel molecular mechanism.
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Affiliation(s)
- Shoude Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China.,Department of Pharmacy, Medical College of Qinghai University, Xining, China.,School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Qiangqiang Jia
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Qiang Gao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Xueru Fan
- Department of Pharmacy, Medical College of Qinghai University, Xining, China
| | - Yuxin Weng
- Department of Pharmacy, Medical College of Qinghai University, Xining, China
| | - Zhanhai Su
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China.,Department of Pharmacy, Medical College of Qinghai University, Xining, China
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14
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Liu J, Wang YL, Zhang JH, Yang JS, Mou HC, Lin J, Yan SJ. Phosphatase CDC25B Inhibitors Produced by Basic Alumina-Supported One-Pot Gram-Scale Synthesis of Fluorinated 2-Alkylthio-4-aminoquinazolines Using Microwave Irradiation. ACS OMEGA 2018; 3:4534-4544. [PMID: 30221227 PMCID: PMC6130795 DOI: 10.1021/acsomega.8b00640] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 04/17/2018] [Indexed: 06/08/2023]
Abstract
An efficient, environmentally benign, and inexpensive procedure has been developed for the synthesis of fluorinated 2-alkylthio-4-aminoquinazolines by microwave irradiation using basic alumina as a solid-support agent as well as a solid base. Notably, this protocol features improved energy efficiency, broad isothiourea substrate scope, easily available starting materials, and high atom efficiency and applicability toward gram-scale synthesis. Additionally, the target compounds were evaluated for the cytotoxic effect against human colon adenocarcinoma (HCT116 and HT29), human gastric cancer (SGC-7901), human lung adenocarcinoma (A549), and human hepatocyte carcinoma (HepG2) cells, and it was found that these compounds have excellent antitumor activities. Among them, compound 3e was found to be one of the most potent derivatives with IC50 values lower than 9.44 μM against five human tumor cell lines, making it more active than cisplatin (DDP). Furthermore, for the first time, the fluorinated 2-alkylthio-substituted 4-aminoquinazolines were identified as phosphatase CDC25B inhibitors.
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Affiliation(s)
- Jin Liu
- Key
Laboratory of Medicinal Chemistry for Natural Resource, Ministry of
Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R.
China
| | - Yu-Ling Wang
- Faculty
of Life Science and Technology, Kunming
University of Science and Technology, Kunming 650504, P. R. China
| | - Ji-Hong Zhang
- Faculty
of Life Science and Technology, Kunming
University of Science and Technology, Kunming 650504, P. R. China
| | - Jian-Shan Yang
- Key
Laboratory of Medicinal Chemistry for Natural Resource, Ministry of
Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R.
China
| | - Han-Chuan Mou
- Faculty
of Life Science and Technology, Kunming
University of Science and Technology, Kunming 650504, P. R. China
| | - Jun Lin
- Key
Laboratory of Medicinal Chemistry for Natural Resource, Ministry of
Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R.
China
| | - Sheng-Jiao Yan
- Key
Laboratory of Medicinal Chemistry for Natural Resource, Ministry of
Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R.
China
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15
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The design of novel inhibitors for treating cancer by targeting CDC25B through disruption of CDC25B-CDK2/Cyclin A interaction using computational approaches. Oncotarget 2018; 8:33225-33240. [PMID: 28402259 PMCID: PMC5464863 DOI: 10.18632/oncotarget.16600] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 03/17/2017] [Indexed: 01/28/2023] Open
Abstract
Cell division cycle 25B is a key cell cycle regulator and widely considered as potent clinical drug target for cancers. This research focused on identifying potential compounds in theory which are able to disrupt transient interactions between CDC25B and its CDK2/Cyclin A substrate.By using the method of ZDOCK and RDOCK, the most optimized 3D structure of CDK2/Cyclin A in complex with CDC25B was constructed and validated using two methods: 1) the superimposition of proteins; 2) analysis of the hydrogen bond distances of Arg 488(N1)-Asp 206(OD1), Arg 492(NE)-Asp 206(OD1), Arg 492(N1)-Asp 206(OD2) and Tyr 497(NE)-Asp 210(OD1). A series of new compounds was gained through searching the fragment database derived from ZINC based on the known inhibitor-compound 7 by the means of "replace fragment" technique. The compounds acquired via meeting the requirements of the absorption, distribution, metabolism, and excretion (ADME) predictions. Finally, 12 compounds with better binding affinity were identified. The comp#1, as a representative, was selected to be synthesized and assayed for their CDC25B inhibitory activities. The comp#1 exhibited mild inhibitory activities against human CDC25B with IC50 values at about 39.02 μM. Molecular Dynamic (MD) simulation revealed that the new inhibitor-comp#1 had favorable conformations for binding to CDC25B and disturbing the interactions between CDC25B and CDK2/Cyclin A.
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16
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Ge Y, van der Kamp M, Malaisree M, Liu D, Liu Y, Mulholland AJ. Identification of the quinolinedione inhibitor binding site in Cdc25 phosphatase B through docking and molecular dynamics simulations. J Comput Aided Mol Des 2017; 31:995-1007. [PMID: 28994029 DOI: 10.1007/s10822-017-0073-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 09/26/2017] [Indexed: 02/02/2023]
Abstract
Cdc25 phosphatase B, a potential target for cancer therapy, is inhibited by a series of quinones. The binding site and mode of quinone inhibitors to Cdc25B remains unclear, whereas this information is important for structure-based drug design. We investigated the potential binding site of NSC663284 [DA3003-1 or 6-chloro-7-(2-morpholin-4-yl-ethylamino)-quinoline-5, 8-dione] through docking and molecular dynamics simulations. Of the two main binding sites suggested by docking, the molecular dynamics simulations only support one site for stable binding of the inhibitor. Binding sites in and near the Cdc25B catalytic site that have been suggested previously do not lead to stable binding in 50 ns molecular dynamics (MD) simulations. In contrast, a shallow pocket between the C-terminal helix and the catalytic site provides a favourable binding site that shows high stability. Two similar binding modes featuring protein-inhibitor interactions involving Tyr428, Arg482, Thr547 and Ser549 are identified by clustering analysis of all stable MD trajectories. The relatively flexible C-terminal region of Cdc25B contributes to inhibitor binding. The binding mode of NSC663284, identified through MD simulation, likely prevents the binding of protein substrates to Cdc25B. The present results provide useful information for the design of quinone inhibitors and their mechanism of inhibition.
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Affiliation(s)
- Yushu Ge
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, People's Republic of China.
- Centre of Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.
| | - Marc van der Kamp
- Centre of Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
- School of Biochemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Maturos Malaisree
- Centre of Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Dan Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Yi Liu
- State Key Laboratory of Virology & Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) & College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
| | - Adrian J Mulholland
- Centre of Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.
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17
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Small molecule targeting of PTPs in cancer. Int J Biochem Cell Biol 2017; 96:171-181. [PMID: 28943273 DOI: 10.1016/j.biocel.2017.09.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/14/2017] [Accepted: 09/15/2017] [Indexed: 01/28/2023]
Abstract
Protein tyrosine phosphatases (PTPs) undeniably have a central role in the development and progression of human cancers. Historically, however, PTPs have not been viewed as privileged drug targets, and progress on identifying potent, selective, and cell-active small molecule PTP inhibitors has suffered accordingly. This situation is rapidly changing, however, due to biochemical advances in the study of PTPs and recent small molecule screening campaigns, which have identified potent and mechanistically diverse lead structures. These compounds are facilitating the exploration of the fundamental cellular processes controlled by PTPs in cancers, and could form the inflection point for new therapeutic paradigms for the treatment of a range of cancers. Herein, we review recent advances in the discovery and biological annotation of cancer-relevant small molecule PTP inhibitors.
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18
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Zwergel C, Czepukojc B, Evain-Bana E, Xu Z, Stazi G, Mori M, Patsilinakos A, Mai A, Botta B, Ragno R, Bagrel D, Kirsch G, Meiser P, Jacob C, Montenarh M, Valente S. Novel coumarin- and quinolinone-based polycycles as cell division cycle 25-A and -C phosphatases inhibitors induce proliferation arrest and apoptosis in cancer cells. Eur J Med Chem 2017; 134:316-333. [DOI: 10.1016/j.ejmech.2017.04.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/03/2017] [Accepted: 04/06/2017] [Indexed: 01/06/2023]
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19
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Arachchige D, Margaret Harris M, Coon Z, Carlsen J, Holub JM. Role of single disulfide linkages in the folding and activity of scyllatoxin-based BH3 domain mimetics. J Pept Sci 2017; 23:367-373. [PMID: 28326661 DOI: 10.1002/psc.2999] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 12/18/2022]
Abstract
Anti-apoptotic Bcl-2 proteins are implicated in pathogenic cell survival and have attracted considerable interest as therapeutic targets. We recently developed a class of synthetic peptide based on scyllatoxin (ScTx) designed to mimic the helical BH3 interaction domain of the pro-apoptotic Bcl-2 protein Bax. In this communication, the contribution of single disulfides in the folding and function of ScTx-Bax peptides was investigated. We synthesized five ScTx-Bax variants, each presenting a different combination of native disulfide linkage and evaluated their ability to directly bind Bcl-2 in vitro. It was determined that the position of the disulfide linkage had significant implications on the structure and function of ScTx-Bax peptides. This study underscores the importance of structural dynamics in BH3:Bcl-2 interactions and further validates ScTx-based ligands as potential modulators of anti-apoptotic Bcl-2 function. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Danushka Arachchige
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - M Margaret Harris
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Zachary Coon
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Jacob Carlsen
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Justin M Holub
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA.,Edison Biotechnology Institute, Ohio University, Athens, OH, 45701, USA.,Molecular and Cellular Biology Program, Ohio University, Athens, OH, 45701, USA
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20
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Sarkis M, Miteva MA, Dasso Lang MC, Jaouen M, Sari MA, Galcéra MO, Ethève-Quelquejeu M, Garbay C, Bertho G, Braud E. Insights into the interaction of high potency inhibitor IRC-083864 with phosphatase CDC25. Proteins 2017; 85:593-601. [PMID: 28056492 DOI: 10.1002/prot.25236] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 12/05/2016] [Accepted: 12/18/2016] [Indexed: 01/11/2023]
Abstract
CDC25 phosphatases play a crucial role in cell cycle regulation. They have been found to be over-expressed in various human tumours and to be valuable targets for cancer treatment. Here, we report the first model of binding of the most potent CDC25 inhibitor to date, the bis-quinone IRC-083864, into CDC25B obtained by combining molecular modeling and NMR studies. Our study provides new insights into key interactions of the catalytic site inhibitor and CDC25B in the absence of any available experimental structure of CDC25 with a bound catalytic site inhibitor. The docking model reveals that IRC-083864 occupies both the active site and the inhibitor binding pocket of the CDC25B catalytic domain. NMR saturation transfer difference and WaterLOGSY data indicate the binding zones of the inhibitor and support the docking model. Probing interactions of analogues of the two quinone units of IRC-083864 with CDC25B demonstrate that IRC-083864 competes with each monomer. Proteins 2017; 85:593-601. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Manal Sarkis
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, CNRS UMR8601, Université Paris Descartes, PRES Sorbonne Paris Cité, Faculté des Sciences Fondamentales et Biomédicales, 45 rue des Saints-Pères, Paris, 75006, France
| | - Maria A Miteva
- Molécules Thérapeutiques in silico, INSERM U973, Université Paris Diderot, PRES Sorbonne Paris Cité, 35 rue Hélène Brion, Paris cedex 13, 75205, France
| | - Maria Chiara Dasso Lang
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, CNRS UMR8601, Université Paris Descartes, PRES Sorbonne Paris Cité, Faculté des Sciences Fondamentales et Biomédicales, 45 rue des Saints-Pères, Paris, 75006, France
| | - Maryse Jaouen
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, CNRS UMR8601, Université Paris Descartes, PRES Sorbonne Paris Cité, Faculté des Sciences Fondamentales et Biomédicales, 45 rue des Saints-Pères, Paris, 75006, France
| | - Marie-Agnès Sari
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, CNRS UMR8601, Université Paris Descartes, PRES Sorbonne Paris Cité, Faculté des Sciences Fondamentales et Biomédicales, 45 rue des Saints-Pères, Paris, 75006, France
| | | | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, CNRS UMR8601, Université Paris Descartes, PRES Sorbonne Paris Cité, Faculté des Sciences Fondamentales et Biomédicales, 45 rue des Saints-Pères, Paris, 75006, France
| | - Christiane Garbay
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, CNRS UMR8601, Université Paris Descartes, PRES Sorbonne Paris Cité, Faculté des Sciences Fondamentales et Biomédicales, 45 rue des Saints-Pères, Paris, 75006, France
| | - Gildas Bertho
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, CNRS UMR8601, Université Paris Descartes, PRES Sorbonne Paris Cité, Faculté des Sciences Fondamentales et Biomédicales, 45 rue des Saints-Pères, Paris, 75006, France
| | - Emmanuelle Braud
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, CNRS UMR8601, Université Paris Descartes, PRES Sorbonne Paris Cité, Faculté des Sciences Fondamentales et Biomédicales, 45 rue des Saints-Pères, Paris, 75006, France
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21
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Phosphatases and kinases regulating CDC25 activity in the cell cycle: clinical implications of CDC25 overexpression and potential treatment strategies. Mol Cell Biochem 2016; 416:33-46. [PMID: 27038604 DOI: 10.1007/s11010-016-2693-2] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 03/24/2016] [Indexed: 10/22/2022]
Abstract
Alterations in the cell-cycle regulatory genes result in uncontrolled cell proliferation leading to several disease conditions. Cyclin-dependent kinases (CDK) and their regulatory subunit, cyclins, are essential proteins in cell-cycle progression. The activity of CDK is regulated by a series of phosphorylation and dephosphorylation at different amino acid residues. Cell Division Cycle-25 (CDC25) plays an important role in transitions between cell-cycle phases by dephosphorylating and activating CDKs. CDC25B and CDC25C play a major role in G2/M progression, whereas CDC25A assists in G1/S transition. Different isomers of CDC25 expressions are upregulated in various clinicopathological situations. Overexpression of CDC25A deregulates G1/S and G2/M events, including the G2 checkpoint. CDC25B has oncogenic properties. Binding to the 14-3-3 proteins regulates the activity and localization of CDC25B. CDC25C is predominantly a nuclear protein in mammalian cells. At the G2/M transition, mitotic activation of CDC25C protein occurs by its dissociation from 14-3-3 proteins along with its phosphorylation at multiple sites within its N-terminal domain. In this article, we critically reviewed the biology of the activation/deactivation of CDC25 by kinases/phosphatases to maintain the level of CDK-cyclin activities and thus the genomic stability, clinical implications due to dysregulation of CDC25, and potential role of CDC25 inhibitors in diseases.
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22
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Winter A, Sigurdardottir AG, DiCara D, Valenti G, Blundell TL, Gherardi E. Developing Antagonists for the Met-HGF/SF Protein–Protein Interaction Using a Fragment-Based Approach. Mol Cancer Ther 2015; 15:3-14. [DOI: 10.1158/1535-7163.mct-15-0446] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/29/2015] [Indexed: 11/16/2022]
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23
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Sheng C, Dong G, Miao Z, Zhang W, Wang W. State-of-the-art strategies for targeting protein-protein interactions by small-molecule inhibitors. Chem Soc Rev 2015; 44:8238-59. [PMID: 26248294 DOI: 10.1039/c5cs00252d] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Targeting protein-protein interactions (PPIs) has emerged as a viable approach in modern drug discovery. However, the identification of small molecules enabling us to effectively interrupt their interactions presents significant challenges. In the recent past, significant advances have been made in the development of new biological and chemical strategies to facilitate the discovery process of small-molecule PPI inhibitors. This review aims to highlight the state-of-the-art technologies and the achievements made recently in this field. The "hot spots" of PPIs have been proved to be critical for small molecules to bind. Three strategies including screening, designing, and synthetic approaches have been explored for discovering PPI inhibitors by targeting the "hot spots". Although the classic high throughput screening approach can be used, fragment screening, fragment-based drug design and newly improved virtual screening are demonstrated to be more effective in the discovery of PPI inhibitors. In addition to screening approaches, design strategies including anchor-based and small molecule mimetics of secondary structures involved in PPIs have become powerful tools as well. Finally, constructing new chemically spaced libraries with high diversity and complexity is becoming an important area of interest for PPI inhibitors. The successful cases from the recent five year studies are used to illustrate how these approaches are implemented to uncover and optimize small molecule PPI inhibitors and notably some of them have become promising therapeutics.
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Affiliation(s)
- Chunquan Sheng
- Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, P. R. China.
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24
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Laraia L, McKenzie G, Spring DR, Venkitaraman AR, Huggins DJ. Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions. CHEMISTRY & BIOLOGY 2015; 22:689-703. [PMID: 26091166 PMCID: PMC4518475 DOI: 10.1016/j.chembiol.2015.04.019] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/01/2015] [Accepted: 04/08/2015] [Indexed: 01/19/2023]
Abstract
Protein-protein interactions (PPIs) underlie the majority of biological processes, signaling, and disease. Approaches to modulate PPIs with small molecules have therefore attracted increasing interest over the past decade. However, there are a number of challenges inherent in developing small-molecule PPI inhibitors that have prevented these approaches from reaching their full potential. From target validation to small-molecule screening and lead optimization, identifying therapeutically relevant PPIs that can be successfully modulated by small molecules is not a simple task. Following the recent review by Arkin et al., which summarized the lessons learnt from prior successes, we focus in this article on the specific challenges of developing PPI inhibitors and detail the recent advances in chemistry, biology, and computation that facilitate overcoming them. We conclude by providing a perspective on the field and outlining four innovations that we see as key enabling steps for successful development of small-molecule inhibitors targeting PPIs.
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Affiliation(s)
- Luca Laraia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Grahame McKenzie
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Ashok R Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - David J Huggins
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK; Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, 19 JJ Thomson Avenue, Cambridge CB3 0HE, UK.
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25
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Fonseca EMB, Trivella DBB, Scorsato V, Dias MP, Bazzo NL, Mandapati KR, de Oliveira FL, Ferreira-Halder CV, Pilli RA, Miranda PCML, Aparicio R. Crystal structures of the apo form and a complex of human LMW-PTP with a phosphonic acid provide new evidence of a secondary site potentially related to the anchorage of natural substrates. Bioorg Med Chem 2015; 23:4462-4471. [PMID: 26117648 DOI: 10.1016/j.bmc.2015.06.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 05/29/2015] [Accepted: 06/05/2015] [Indexed: 12/22/2022]
Abstract
Low molecular weight protein tyrosine phosphatases (LMW-PTP, EC 3.1.3.48) are a family of single-domain enzymes with molecular weight up to 18 kDa, expressed in different tissues and considered attractive pharmacological targets for cancer chemotherapy. Despite this, few LMW-PTP inhibitors have been described to date, and the structural information on LMW-PTP druggable binding sites is scarce. In this study, a small series of phosphonic acids were designed based on a new crystallographic structure of LMW-PTP complexed with benzylsulfonic acid, determined at 2.1Å. In silico docking was used as a tool to interpret the structural and enzyme kinetics data, as well as to design new analogs. From the synthesized series, two compounds were found to act as competitive inhibitors, with inhibition constants of 0.124 and 0.047 mM. We also report the 2.4Å structure of another complex in which LMW-PTP is bound to benzylphosphonic acid, and a structure of apo LMW-PTP determined at 2.3Å resolution. Although no appreciable conformation changes were observed, in the latter structures, amino acid residues from an expression tag were found bound to a hydrophobic region at the protein surface. This regions is neighbored by positively charged residues, adjacent to the active site pocket, suggesting that this region might be not a mere artefact of crystal contacts but an indication of a possible anchoring region for the natural substrate-which is a phosphorylated protein.
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Affiliation(s)
- Emanuella M B Fonseca
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP 6154, 13083-970, Campinas, SP, Brazil
| | - Daniela B B Trivella
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP 6154, 13083-970, Campinas, SP, Brazil; Department of Organic Chemistry, Institute of Chemistry, University of Campinas, CP 6154, CEP 13083-970, Campinas, SP, Brazil
| | - Valéria Scorsato
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP 6154, 13083-970, Campinas, SP, Brazil
| | - Mariana P Dias
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP 6154, 13083-970, Campinas, SP, Brazil
| | - Natália L Bazzo
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP 6154, 13083-970, Campinas, SP, Brazil
| | - Kishore R Mandapati
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP 6154, 13083-970, Campinas, SP, Brazil; Department of Organic Chemistry, Institute of Chemistry, University of Campinas, CP 6154, CEP 13083-970, Campinas, SP, Brazil
| | - Fábio L de Oliveira
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP 6154, 13083-970, Campinas, SP, Brazil
| | - Carmen V Ferreira-Halder
- Department of Biochemistry, Institute of Biology, University of Campinas, CEP 13083-862, Campinas, SP, Brazil
| | - Ronaldo A Pilli
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, CP 6154, CEP 13083-970, Campinas, SP, Brazil
| | - Paulo C M L Miranda
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, CP 6154, CEP 13083-970, Campinas, SP, Brazil
| | - Ricardo Aparicio
- Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP 6154, 13083-970, Campinas, SP, Brazil.
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Hirai G, Sodeoka M. Focused library with a core structure extracted from natural products and modified: application to phosphatase inhibitors and several biochemical findings. Acc Chem Res 2015; 48:1464-73. [PMID: 25894598 DOI: 10.1021/acs.accounts.5b00048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Synthesis of a focused library is an important strategy to create novel modulators of specific classes of proteins. Compounds in a focused library are composed of a common core structure and different diversity structures. In this Account, we describe our design and synthesis of libraries focused on selective inhibitors of protein phosphatases (PPases). We considered that core structures having structural and electronic features similar to those of PPase substrates, phosphate esters, would be a reasonable choice. Therefore, we extracted core structures from natural products already identified as PPase inhibitors. Since many PPases share similar active-site structures, such phosphate-mimicking core structures should interact with many enzymes in the same family, and therefore the choice of diversity structures is pivotal both to increase the binding affinity and to achieve specificity for individual enzymes. Here we present case studies of application of focused libraries to obtain PPase inhibitors, covering the overall process from selection of core structures to identification and evaluation of candidates in the focused libraries. To synthesize a library focused on protein serine-threonine phosphatases (PPs), we chose norcantharidin as a core structure, because norcantharidin dicarboxylate shows a broad inhibition profile toward several PPs. From the resulting focused library, we identified a highly selective PP2B inhibitor, NCA-01. On the other hand, to find inhibitors of dual-specificity protein phosphatases (DSPs), we chose 3-acyltetronic acid extracted from natural product RK-682 as a core structure, because its structure resembles the transition state in the dephosphorylation reaction of DSPs. However, a highly selective inhibitor was not found in the resulting focused library. Furthermore, an inherent drawback of compounds having the highly acidic 3-acyltetronic acid as a core structure is very weak potency in cellulo, probably due to poor cell membrane permeability. Therefore, we next modified the core structure from acidic to neutral by transformation to the enamine derivative and constructed a second-generation focused library (RE derivatives). The resulting compounds showed dramatically improved cell membrane permeability and inhibitory selectivity and included VHR (vaccinia VH1-related)-selective RE12 and CDC25A/B (cell division cycle 25A/B)-selective RE44. These inhibitors act on target enzymes in cellulo and do not generate reactive oxygen species, which is a potential problem with quinoid-type inhibitors of CDC25s. The cellular activity of RE12 was further improved by replacement of the side chain to afford RE176, which showed more potent antiproliferative activity than RE12 against HeLa cells. The dramatic change of inhibitory selectivity obtained by core structure modification from 3-acyltetronic acid to its enamine derivative was associated with a change in the mode of action. Namely, RE derivatives were found to be noncompetitive inhibitors with respect to a small-molecular substrate of CDC25A/B, whereas RK-682 was a competitive inhibitor of VHR. We identified the binding site of RE derivatives on the CDC25A as a pocket adjacent to the active site; this appears to be a promising target site for development of further novel inhibitors of CDC25s.
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Affiliation(s)
- Go Hirai
- Synthetic Organic Chemistry
Laboratory, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- CREST-JST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry
Laboratory, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- CREST-JST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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Zhang S, Shi Y, Wang W, Yuan Z. Study on the association between CTD peptides and zinc(ii)-dipicolylamine appended beta-cyclodextrin. RSC Adv 2015. [DOI: 10.1039/c5ra12374g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Association between zinc(ii)-dipicolylamine appended beta-cyclodextrin and CTD (carboxy-terminal domain of RNA polymerase II) peptides with different phosphorylation patterns was studied by ITC and NMR.
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Affiliation(s)
- Saihui Zhang
- Key Laboratory of Functional Polymer Materials of Ministry of Education
- Institute of Polymer Chemistry
- Nankai University and Collaborative Innovation Center of Chemical Science and Engineering
- Nankai University
- Tianjin 300071
| | - Yantao Shi
- Key Laboratory of Functional Polymer Materials of Ministry of Education
- Institute of Polymer Chemistry
- Nankai University and Collaborative Innovation Center of Chemical Science and Engineering
- Nankai University
- Tianjin 300071
| | - Wei Wang
- Key Laboratory of Functional Polymer Materials of Ministry of Education
- Institute of Polymer Chemistry
- Nankai University and Collaborative Innovation Center of Chemical Science and Engineering
- Nankai University
- Tianjin 300071
| | - Zhi Yuan
- Key Laboratory of Functional Polymer Materials of Ministry of Education
- Institute of Polymer Chemistry
- Nankai University and Collaborative Innovation Center of Chemical Science and Engineering
- Nankai University
- Tianjin 300071
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