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Almukadi H, Jadkarim GA, Mohammed A, Almansouri M, Sultana N, Shaik NA, Banaganapalli B. Combining machine learning and structure-based approaches to develop oncogene PIM kinase inhibitors. Front Chem 2023; 11:1137444. [PMID: 36970406 PMCID: PMC10036574 DOI: 10.3389/fchem.2023.1137444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/09/2023] [Indexed: 03/12/2023] Open
Abstract
Introduction: PIM kinases are targets for therapeutic intervention since they are associated with a number of malignancies by boosting cell survival and proliferation. Over the past years, the rate of new PIM inhibitors discovery has increased significantly, however, new generation of potent molecules with the right pharmacologic profiles were in demand that can probably lead to the development of Pim kinase inhibitors that are effective against human cancer.Method: In the current study, a machine learning and structure based approaches were used to generate novel and effective chemical therapeutics for PIM-1 kinase. Four different machine learning methods, namely, support vector machine, random forest, k-nearest neighbour and XGBoost have been used for the development of models. Total, 54 Descriptors have been selected using the Boruta method.Results: SVM, Random Forest and XGBoost shows better performance as compared to k-NN. An ensemble approach was implemented and, finally, four potential molecules (CHEMBL303779, CHEMBL690270, MHC07198, and CHEMBL748285) were found to be effective for the modulation of PIM-1 activity. Molecular docking and molecular dynamic simulation corroborated the potentiality of the selected molecules. The molecular dynamics (MD) simulation study indicated the stability between protein and ligands.Discussion: Our findings suggest that the selected models are robust and can be potentially useful for facilitating the discovery against PIM kinase.
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Affiliation(s)
- Haifa Almukadi
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Gada Ali Jadkarim
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Arif Mohammed
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Majid Almansouri
- Department of Clinical Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nasreen Sultana
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
- *Correspondence: Noor Ahmad Shaik, ; Nasreen Sultana, ; Babajan Banaganapalli,
| | - Noor Ahmad Shaik
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- *Correspondence: Noor Ahmad Shaik, ; Nasreen Sultana, ; Babajan Banaganapalli,
| | - Babajan Banaganapalli
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- *Correspondence: Noor Ahmad Shaik, ; Nasreen Sultana, ; Babajan Banaganapalli,
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Lazinski LM, Royal G, Robin M, Maresca M, Haudecoeur R. Bioactive Aurones, Indanones, and Other Hemiindigoid Scaffolds: Medicinal Chemistry and Photopharmacology Perspectives. J Med Chem 2022; 65:12594-12625. [PMID: 36126323 DOI: 10.1021/acs.jmedchem.2c01150] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hemiindigoids comprise a range of natural and synthetic scaffolds that share the same aromatic hydrocarbon backbone as well as promising biological and optical properties. The encouraging therapeutic potential of these scaffolds has been unraveled by many studies over the past years and uncovered representants with inspiring pharmacophoric features such as the acetylcholinesterase inhibitor donezepil and the tubulin polymerization inhibitor indanocine. In this review, we summarize the last advances in the medicinal potential of hemiindigoids, with a special attention to molecular design, structure-activity relationship, ligand-target interactions, and mechanistic explanations covering their effects. As their strong fluorogenic potential and photoswitch behavior recently started to be highlighted and explored in biology, giving rise to the development of novel fluorescent probes and photopharmacological agents, we also discuss these properties in a medicinal chemistry perspective.
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Affiliation(s)
- Leticia M Lazinski
- Université Grenoble Alpes, CNRS 5063, DPM, 38000 Grenoble, France.,Université Grenoble Alpes, CNRS 5250, DCM, 38000 Grenoble, France
| | - Guy Royal
- Université Grenoble Alpes, CNRS 5250, DCM, 38000 Grenoble, France
| | - Maxime Robin
- Mediterranean Institute of Marine and Terrestrial Biodiversity and Ecology (IMBE), Aix Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille, France
| | - Marc Maresca
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, 13397 Marseille, France
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Through Diffusion Measurements of Molecules to a Numerical Model for Protein Crystallization in Viscous Polyethylene Glycol Solution. CRYSTALS 2022. [DOI: 10.3390/cryst12070881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Protein crystallography has become a popular method for biochemists, but obtaining high-quality protein crystals for precise structural analysis and larger ones for neutron analysis requires further technical progress. Many studies have noted the importance of solvent viscosity for the probability of crystal nucleation and for mass transportation; therefore, in this paper, we have reported on experimental results and simulation studies regarding the use of viscous polyethylene glycol (PEG) solvents for protein crystals. We investigated the diffusion rates of proteins, peptides, and small molecules in viscous PEG solvents using fluorescence correlation spectroscopy. In high-molecular-weight PEG solutions (molecular weights: 10,000 and 20,000), solute diffusion showed deviations, with a faster diffusion than that estimated by the Stokes–Einstein equation. We showed that the extent of the deviation depends on the difference between the molecular sizes of the solute and PEG solvent, and succeeded in creating equations to predict diffusion coefficients in viscous PEG solutions. Using these equations, we have developed a new numerical model of 1D diffusion processes of proteins and precipitants in a counter-diffusion chamber during crystallization processes. Examples of the application of anomalous diffusion in counter-diffusion crystallization are shown by the growth of lysozyme crystals.
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Zhao Y, Aziz AUR, Zhang H, Zhang Z, Li N, Liu B. A systematic review on active sites and functions of PIM-1 protein. Hum Cell 2022; 35:427-440. [PMID: 35000143 DOI: 10.1007/s13577-021-00656-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022]
Abstract
The Proviral Integration of Molony murine leukemia virus (PIM)-1 protein contributes to the solid cancers and hematologic malignancies, cell growth, proliferation, differentiation, migration, and other life activities. Many studies have related these functions to its molecular structure, subcellular localization and expression level. However, recognition of specific active sites and their effects on the activity of this constitutively active kinase is still a challenge. Based on the close relationship between its molecular structure and functional activity, this review covers the specific residues involved in the binding of ATP and different substrates in its catalytic domain. This review then elaborates on the relevant changes in protein conformation and cell functions after PIM-1 binds to different substrates. Therefore, this intensive study can improve the understanding of PIM-1-regulated signaling pathways by facilitating the discovery of its potential phosphorylation substrates.
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Affiliation(s)
- Youyi Zhao
- School of Biomedical Engineering, Liaoning Key Lab of Integrated Circuit and Biomedical Electronic System, Dalian University of Technology, Dalian, 116024, China
| | - Aziz Ur Rehman Aziz
- School of Biomedical Engineering, Liaoning Key Lab of Integrated Circuit and Biomedical Electronic System, Dalian University of Technology, Dalian, 116024, China
| | - Hangyu Zhang
- School of Biomedical Engineering, Liaoning Key Lab of Integrated Circuit and Biomedical Electronic System, Dalian University of Technology, Dalian, 116024, China
| | - Zhengyao Zhang
- School of Life and Pharmaceutical Sciences, Panjin Campus of Dalian University of Technology, Panjin, 124221, China
| | - Na Li
- School of Biomedical Engineering, Liaoning Key Lab of Integrated Circuit and Biomedical Electronic System, Dalian University of Technology, Dalian, 116024, China.
| | - Bo Liu
- School of Biomedical Engineering, Liaoning Key Lab of Integrated Circuit and Biomedical Electronic System, Dalian University of Technology, Dalian, 116024, China.
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Crystal Structure-Guided Design of Bisubstrate Inhibitors and Photoluminescent Probes for Protein Kinases of the PIM Family. Molecules 2021; 26:molecules26144353. [PMID: 34299628 PMCID: PMC8307404 DOI: 10.3390/molecules26144353] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/09/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
We performed an X-ray crystallographic study of complexes of protein kinase PIM-1 with three inhibitors comprising an adenosine mimetic moiety, a linker, and a peptide-mimetic (d-Arg)6 fragment. Guided by the structural models, simplified chemical structures with a reduced number of polar groups and chiral centers were designed. The developed inhibitors retained low-nanomolar potency and possessed remarkable selectivity toward the PIM kinases. The new inhibitors were derivatized with biotin or fluorescent dye Cy5 and then applied for the detection of PIM kinases in biochemical solutions and in complex biological samples. The sandwich assay utilizing a PIM-2-selective detection antibody featured a low limit of quantification (44 pg of active recombinant PIM-2). Fluorescent probes were efficiently taken up by U2OS cells and showed a high extent of co-localization with PIM-1 fused with a fluorescent protein. Overall, the developed inhibitors and derivatives represent versatile chemical tools for studying PIM function in cellular systems in normal and disease physiology.
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Park H, Jeon J, Kim K, Choi S, Hong S. Structure-Based Virtual Screening and De Novo Design of PIM1 Inhibitors with Anticancer Activity from Natural Products. Pharmaceuticals (Basel) 2021; 14:ph14030275. [PMID: 33803840 PMCID: PMC8003278 DOI: 10.3390/ph14030275] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND the proviral insertion site of Moloney murine leukemia (PIM) 1 kinase has served as a therapeutic target for various human cancers due to the enhancement of cell proliferation and the inhibition of apoptosis. METHODS to identify effective PIM1 kinase inhibitors, structure-based virtual screening of natural products of plant origin and de novo design were carried out using the protein-ligand binding free energy function improved by introducing an adequate dehydration energy term. RESULTS as a consequence of subsequent enzyme inhibition assays, four classes of PIM1 kinase inhibitors were discovered, with the biochemical potency ranging from low-micromolar to sub-micromolar levels. The results of extensive docking simulations showed that the inhibitory activity stemmed from the formation of multiple hydrogen bonds in combination with hydrophobic interactions in the ATP-binding site. Optimization of the biochemical potency by chemical modifications of the 2-benzylidenebenzofuran-3(2H)-one scaffold led to the discovery of several nanomolar inhibitors with antiproliferative activities against human breast cancer cell lines. CONCLUSIONS these new PIM1 kinase inhibitors are anticipated to serve as a new starting point for the development of anticancer medicine.
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Affiliation(s)
- Hwangseo Park
- Department of Bioscience and Biotechnology and Institute of Anticancer Medicine Development, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul 05006, Korea
- Correspondence: (H.P.); (S.H.); Tel.: +82-23-408-3766 (H.P.); +82-42-350-2811 (S.H.)
| | - Jinwon Jeon
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea; (J.J.); (K.K.); (S.C.)
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Kewon Kim
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea; (J.J.); (K.K.); (S.C.)
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Soyeon Choi
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea; (J.J.); (K.K.); (S.C.)
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Sungwoo Hong
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea; (J.J.); (K.K.); (S.C.)
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Correspondence: (H.P.); (S.H.); Tel.: +82-23-408-3766 (H.P.); +82-42-350-2811 (S.H.)
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Alnabulsi S, Al-Hurani EA. Pim kinase inhibitors in cancer: medicinal chemistry insights into their activity and selectivity. Drug Discov Today 2020; 25:S1359-6446(20)30374-3. [PMID: 32971234 DOI: 10.1016/j.drudis.2020.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/09/2020] [Accepted: 09/14/2020] [Indexed: 01/09/2023]
Abstract
The oncogenic Pim kinase proteins (Pim-1/2/3) regulate tumorigenesis through phosphorylating essential proteins that control cell cycle and proliferation. Pim kinase is a potential chemotherapeutic target in cancer and its inhibition is currently the focus of intensive drug design and development efforts. The distinctive presence of proline amino acids in the hinge region provides an opportunity to inhibit Pim kinase while conserving the physiological functions of other kinases and reducing the toxicity profiles of the inhibitors. Various Pim kinase inhibitors have been clinically evaluated for the treatment of hematological cancers, yet none has reached the clinic. In this review, we discuss the design and development of selective and potent Pim inhibitors with novel chemotypes focusing on structural features essential for high potency and selectivity.
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Affiliation(s)
- Soraya Alnabulsi
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, PO Box 3030, Irbid 22110, Jordan.
| | - Enas A Al-Hurani
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, PO Box 3030, Irbid 22110, Jordan
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PIM1, CYP1B1, and HSPA2 Targeted by Quercetin Play Important Roles in Osteoarthritis Treatment by Achyranthes bidentata. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2019; 2019:1205942. [PMID: 31998395 PMCID: PMC6964619 DOI: 10.1155/2019/1205942] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/18/2019] [Indexed: 01/02/2023]
Abstract
Aim Achyranthes bidentata is one of the most commonly used Chinese herbal medicines (CHM) that is currently considered for the treatment of osteoarthritis. The purpose of this study was to reveal the mechanism of Achyranthes bidentata in osteoarthritis treatment based on the network pharmacology. Methods The effective components of Achyranthes bidentata were firstly screened out from the TCMSP database with ADME property parameters. Then, osteoarthritis-related proteins targeted by the effective components were predicted based on the DrugBank and CTD databases. Subsequently, enrichment analysis and interaction network between targets of effective components and pathways were also studied. In addition, the differentially expressed genes (DEGs) of GSE55457 were used for validation of the osteoarthritis-related target proteins. Finally, the effective components-target molecular docking models were predicted. Results A total of 10 effective components were identified, of which kaempferol and quercetin had 1 and 29 targets, respectively. There were 26 target proteins of quercetin related to the osteoarthritis. These targets were mainly enriched in mitochondrial ATP synthesis coupled proton transport, cellular response to estradiol stimulus, and nitric oxide biosynthetic process. In addition, there were three common proteins, PIM1, CYP1B1, and HSPA2 based on the DEGs of GSE55457, which were considered as the key targeted proteins of the quercetin. Conclusion The docking of PIM1-quercetin, CYP1B1-quercetin, and HSPA2-quercetin may play important roles during the treatment of osteoarthritis by Achyranthes bidentata.
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Su D, Hou Y, Dong C, Ren J. Fluctuation correlation spectroscopy and its applications in homogeneous analysis. Anal Bioanal Chem 2019; 411:4523-4540. [DOI: 10.1007/s00216-019-01884-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/12/2019] [Accepted: 04/29/2019] [Indexed: 12/11/2022]
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10
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Wang X, Sun Z. Understanding PIM-1 kinase inhibitor interactions with free energy simulation. Phys Chem Chem Phys 2019; 21:7544-7558. [PMID: 30895980 DOI: 10.1039/c9cp00070d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The proviral integration site of the Moloney leukemia virus (PIM) family includes three homologous members. PIM-1 kinase is an important target in effective therapeutic interventions of lymphomas, prostate cancer and leukemia. In the current work, we performed free energy calculations to calculate the binding affinities of several inhibitors targeting this protein. The alchemical method with integration and perturbation-based estimators and the end-point methods were compared. The computational results indicated that the alchemical method can accurately predict the binding affinities, while the end-point methods give relatively unreliable predictions. Decomposing the free energy difference into enthalpic and entropic components with MBAR reweighting enabled us to investigate the detailed thermodynamic parameters with which the entropy-enthalpy compensation in this protein-ligand binding case is identified. We then studied the conformational ensemble, and the important protein-ligand interactions were identified. The current work sheds light on the understanding of the PIM-1-kinase-inhibitor interactions at the atomic level and will be useful in the further development of potential drugs.
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Affiliation(s)
- Xiaohui Wang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
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11
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Katsura K, Tomabechi Y, Matsuda T, Yonemochi M, Mikuni J, Ohsawa N, Terada T, Yokoyama S, Kukimoto-Niino M, Takemoto C, Shirouzu M. Phosphorylated and non-phosphorylated HCK kinase domains produced by cell-free protein expression. Protein Expr Purif 2018; 150:92-99. [PMID: 29793032 DOI: 10.1016/j.pep.2018.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/10/2018] [Accepted: 05/10/2018] [Indexed: 01/07/2023]
Abstract
Since phosphorylation is involved in various physiological events, kinases and interacting factors can be potential targets for drug discovery. For the development and improvement of inhibitors from the point of view of mechanistic enzymology, a cell-free protein synthesis system would be advantageous, since it could prepare mutant proteins easily. However, especially in the case of protein kinase, product solubility remains one of the major challenges. To overcome this problem, we prepared a chaperone-supplemented extract from Escherichia coli BL21 cells harboring a plasmid encoding a set of chaperone genes, dnaK, dnaJ, and grpE. We explored cell-disruption procedures and constructed an efficient protein synthesis system. Employing this system, we produced the kinase domain of human hematopoietic cell kinase (HCK) to obtain further structural information about its molecular interaction with one of its inhibitors, previously developed by our group (RK-20449). Lower reaction temperature improved the solubility, and addition of a protein phosphatase (YpoH) facilitated the homogeneous production of the non-phosphorylated kinase domain. Crystals of the purified product were obtained and the kinase-inhibitor complex structure was solved at 1.7 Å resolution. In addition, results of kinase activity measurement, using a synthetic substrate, showed that the kinase activity was facilitated by autophosphorylation at Tyr416, as confirmed by the peptide mass mapping.
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Affiliation(s)
- Kazushige Katsura
- Protein Functional and Structural Biology Team, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yuri Tomabechi
- Protein Functional and Structural Biology Team, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takayoshi Matsuda
- Protein Functional and Structural Biology Team, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mayumi Yonemochi
- Protein Functional and Structural Biology Team, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Drug Discovery Structural Biology Platform Unit, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Junko Mikuni
- Protein Functional and Structural Biology Team, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Drug Discovery Structural Biology Platform Unit, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Noboru Ohsawa
- Protein Functional and Structural Biology Team, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takaho Terada
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mutsuko Kukimoto-Niino
- Protein Functional and Structural Biology Team, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Drug Discovery Structural Biology Platform Unit, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Chie Takemoto
- Protein Functional and Structural Biology Team, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Mikako Shirouzu
- Protein Functional and Structural Biology Team, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Drug Discovery Structural Biology Platform Unit, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
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Watanabe C, Watanabe H, Fukuzawa K, Parker LJ, Okiyama Y, Yuki H, Yokoyama S, Nakano H, Tanaka S, Honma T. Theoretical Analysis of Activity Cliffs among Benzofuranone-Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson-Boltzmann Surface Area (FMO+MM-PBSA) Approach. J Chem Inf Model 2017; 57:2996-3010. [PMID: 29111719 DOI: 10.1021/acs.jcim.7b00110] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Significant activity changes due to small structural changes (i.e., activity cliffs) of serine/threonine kinase Pim1 inhibitors were studied theoretically using the fragment molecular orbital method with molecular mechanics Poisson-Boltzmann surface area (FMO+MM-PBSA) approach. This methodology enables quantum-chemical calculations for large biomolecules with solvation. In the course of drug discovery targeting Pim1, six benzofuranone-class inhibitors were found to differ only in the position of the indole-ring nitrogen atom. By comparing the various qualities of complex structures based on X-ray, classical molecular mechanics (MM)-optimized, and quantum/molecular mechanics (QM/MM)-optimized structures, we found that the QM/MM-optimized structures provided the best correlation (R2 = 0.85) between pIC50 and the calculated FMO+MM-PBSA binding energy. Combining the classical solvation energy with the QM binding energy was important to increase the correlation. In addition, decomposition of the interaction energy into various physicochemical components by pair interaction energy decomposition analysis suggested that CH-π and electrostatic interactions mainly caused the activity differences.
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Affiliation(s)
- Chiduru Watanabe
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Institute of Industrial Science, The University of Tokyo , 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Hirofumi Watanabe
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kaori Fukuzawa
- Institute of Industrial Science, The University of Tokyo , 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan.,Department of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University , 2-4-41 Ebara, Shinagawa, Tokyo 142-8501, Japan
| | - Lorien J Parker
- RIKEN Structural Biology Laboratory , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Department of Structural Biology, St. Vincent's Institute , 9 Princes Street, Fitzroy, Victoria 3065, Australia
| | - Yoshio Okiyama
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hitomi Yuki
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Structural Biology Laboratory , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hirofumi Nakano
- Drug Discovery Initiative, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shigenori Tanaka
- Graduate School of System Informatics, Kobe University , 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Teruki Honma
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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Koda Y, Kikuzato K, Mikuni J, Tanaka A, Yuki H, Honma T, Tomabechi Y, Kukimoto-Niino M, Shirouzu M, Shirai F, Koyama H. Identification of pyrrolo[2,3- d ]pyrimidines as potent HCK and FLT3-ITD dual inhibitors. Bioorg Med Chem Lett 2017; 27:4994-4998. [DOI: 10.1016/j.bmcl.2017.10.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 10/06/2017] [Accepted: 10/07/2017] [Indexed: 11/15/2022]
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Breen ME, Soellner MB. Small molecule substrate phosphorylation site inhibitors of protein kinases: approaches and challenges. ACS Chem Biol 2015; 10:175-89. [PMID: 25494294 PMCID: PMC4301090 DOI: 10.1021/cb5008376] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Protein kinases are
important mediators of cellular communication
and attractive drug targets for many diseases. Although success has
been achieved with developing ATP-competitive kinase inhibitors, the
disadvantages of ATP-competitive inhibitors have led to increased
interest in targeting sites outside of the ATP binding pocket. Kinase
inhibitors with substrate-competitive, ATP-noncompetitive binding
modes are promising due to the possibility of increased selectivity
and better agreement between biochemical and in vitro potency. However, the difficulty of identifying these types of inhibitors
has resulted in significantly fewer small molecule substrate phosphorylation
site inhibitors being reported compared to ATP-competitive inhibitors.
This review surveys reported substrate phosphorylation site inhibitors
and methods that can be applied to the discovery of such inhibitors,
including a discussion of the challenges inherent to these screening
methods.
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Affiliation(s)
- Meghan E. Breen
- Department of Medicinal Chemistry and ‡Department of
Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Matthew B. Soellner
- Department of Medicinal Chemistry and ‡Department of
Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
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15
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Niwa H, Mikuni J, Sasaki S, Tomabechi Y, Honda K, Ikeda M, Ohsawa N, Wakiyama M, Handa N, Shirouzu M, Honma T, Tanaka A, Yokoyama S. Crystal structures of the S6K1 kinase domain in complexes with inhibitors. ACTA ACUST UNITED AC 2014; 15:153-64. [PMID: 25078151 PMCID: PMC4125821 DOI: 10.1007/s10969-014-9188-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 07/15/2014] [Indexed: 11/30/2022]
Abstract
Ribosomal protein S6 kinase 1 (S6K1) is a serine/threonine protein kinase that plays an important role in the PIK3/mTOR signaling pathway, and is implicated in diseases including diabetes, obesity, and cancer. The crystal structures of the S6K1 kinase domain in complexes with staurosporine and the S6K1-specific inhibitor PF-4708671 have been reported. In the present study, five compounds (F108, F109, F176, F177, and F179) were newly identified by in silico screening of a chemical library and kinase assay. The crystal structures of the five inhibitors in complexes with the S6K1 kinase domain were determined at resolutions between 1.85 and 2.10 Å. All of the inhibitors bound to the ATP binding site, lying along the P-loop, while the activation loop stayed in the inactive form. Compound F179, with a carbonyl group in the middle of the molecule, altered the αC helix conformation by interacting with the invariant Lys123. Compounds F176 and F177 bound slightly distant from the hinge region, and their sulfoamide groups formed polar interactions with the protein. The structural features required for the specific binding of inhibitors are discussed.
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Affiliation(s)
- Hideaki Niwa
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
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16
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Foulks JM, Carpenter KJ, Luo B, Xu Y, Senina A, Nix R, Chan A, Clifford A, Wilkes M, Vollmer D, Brenning B, Merx S, Lai S, McCullar MV, Ho KK, Albertson DJ, Call LT, Bearss JJ, Tripp S, Liu T, Stephens BJ, Mollard A, Warner SL, Bearss DJ, Kanner SB. A small-molecule inhibitor of PIM kinases as a potential treatment for urothelial carcinomas. Neoplasia 2014; 16:403-12. [PMID: 24953177 PMCID: PMC4198696 DOI: 10.1016/j.neo.2014.05.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/12/2014] [Accepted: 05/13/2014] [Indexed: 11/30/2022]
Abstract
The proto-oncogene proviral integration site for moloney murine leukemia virus (PIM) kinases (PIM-1, PIM-2, and PIM-3) are serine/threonine kinases that are involved in a number of signaling pathways important to cancer cells. PIM kinases act in downstream effector functions as inhibitors of apoptosis and as positive regulators of G1-S phase progression through the cell cycle. PIM kinases are upregulated in multiple cancer indications, including lymphoma, leukemia, multiple myeloma, and prostate, gastric, and head and neck cancers. Overexpression of one or more PIM family members in patient tumors frequently correlates with poor prognosis. The aim of this investigation was to evaluate PIM expression in low- and high-grade urothelial carcinoma and to assess the role PIM function in disease progression and their potential to serve as molecular targets for therapy. One hundred thirty-seven cases of urothelial carcinoma were included in this study of surgical biopsy and resection specimens. High levels of expression of all three PIM family members were observed in both noninvasive and invasive urothelial carcinomas. The second-generation PIM inhibitor, TP-3654, displays submicromolar activity in pharmacodynamic biomarker modulation, cell proliferation studies, and colony formation assays using the UM-UC-3 bladder cancer cell line. TP-3654 displays favorable human ether-à-go-go-related gene and cytochrome P450 inhibition profiles compared with the first-generation PIM inhibitor, SGI-1776, and exhibits oral bioavailability. In vivo xenograft studies using a bladder cancer cell line show that PIM kinase inhibition can reduce tumor growth, suggesting that PIM kinase inhibitors may be active in human urothelial carcinomas.
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Affiliation(s)
| | | | - Bai Luo
- Astex Pharmaceuticals, Inc, Salt Lake City, UT
| | - Yong Xu
- Astex Pharmaceuticals, Inc, Salt Lake City, UT
| | - Anna Senina
- Astex Pharmaceuticals, Inc, Salt Lake City, UT
| | - Rebecca Nix
- Astex Pharmaceuticals, Inc, Salt Lake City, UT
| | - Ashley Chan
- Astex Pharmaceuticals, Inc, Salt Lake City, UT
| | | | | | | | | | | | - Shuping Lai
- Astex Pharmaceuticals, Inc, Salt Lake City, UT
| | | | - Koc-Kan Ho
- Astex Pharmaceuticals, Inc, Salt Lake City, UT
| | - Daniel J Albertson
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
| | | | - Jared J Bearss
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | | | - Ting Liu
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
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17
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Parker LJ, Taruya S, Tsuganezawa K, Ogawa N, Mikuni J, Honda K, Tomabechi Y, Handa N, Shirouzu M, Yokoyama S, Tanaka A. Kinase crystal identification and ATP-competitive inhibitor screening using the fluorescent ligand SKF86002. ACTA ACUST UNITED AC 2014; 70:392-404. [PMID: 24531473 DOI: 10.1107/s1399004713028654] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 10/17/2013] [Indexed: 11/10/2022]
Abstract
The small kinase inhibitor SKF86002 lacks intrinsic fluorescence but becomes fluorescent upon binding to the ATP-binding sites of p38 mitogen-activated protein kinase (p38α). It was found that co-crystals of this compound with various kinases were distinguishable by their strong fluorescence. The co-crystals of SKF86002 with p38α, Pim1, ASK1, HCK and AMPK were fluorescent. Addition of SKF86002, which binds to the ATP site, to the co-crystallization solution of HCK promoted protein stability and thus facilitated the production of crystals that otherwise would not grow in the apo form. It was further demonstrated that the fluorescence of SKF86002 co-crystals can be applied to screen for candidate kinase inhibitors. When a compound binds competitively to the ATP-binding site of a kinase crystallized with SKF86002, it displaces the fluorescent SKF86002 and the crystal loses its fluorescence. Lower fluorescent signals were reported after soaking SKF86002-Pim1 and SKF86002-HCK co-crystals with the inhibitors quercetin, a quinazoline derivative and A-419259. Determination of the SKF86002-Pim1 and SKF86002-HCK co-crystal structures confirmed that SKF86002 interacts with the ATP-binding sites of Pim1 and HCK. The structures of Pim1-SKF86002 crystals soaked with the inhibitors quercetin and a quinazoline derivative and of HCK-SKF86002 crystals soaked with A-419259 were determined. These structures were virtually identical to the deposited crystal structures of the same complexes. A KINOMEscan assay revealed that SKF86002 binds a wide variety of kinases. Thus, for a broad range of kinases, SKF86002 is useful as a crystal marker, a crystal stabilizer and a marker to identify ligand co-crystals for structural analysis.
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Affiliation(s)
- Lorien J Parker
- Systems and Structural Biology Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Shigenao Taruya
- Systems and Structural Biology Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Keiko Tsuganezawa
- Systems and Structural Biology Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Naoko Ogawa
- Systems and Structural Biology Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Junko Mikuni
- Systems and Structural Biology Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Keiko Honda
- Systems and Structural Biology Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Yuri Tomabechi
- Systems and Structural Biology Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Noriko Handa
- Systems and Structural Biology Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Mikako Shirouzu
- Systems and Structural Biology Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- Systems and Structural Biology Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Akiko Tanaka
- Systems and Structural Biology Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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18
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Saito Y, Yuki H, Kuratani M, Hashizume Y, Takagi S, Honma T, Tanaka A, Shirouzu M, Mikuni J, Handa N, Ogahara I, Sone A, Najima Y, Tomabechi Y, Wakiyama M, Uchida N, Tomizawa-Murasawa M, Kaneko A, Tanaka S, Suzuki N, Kajita H, Aoki Y, Ohara O, Shultz LD, Fukami T, Goto T, Taniguchi S, Yokoyama S, Ishikawa F. A pyrrolo-pyrimidine derivative targets human primary AML stem cells in vivo. Sci Transl Med 2013; 5:181ra52. [PMID: 23596204 DOI: 10.1126/scitranslmed.3004387] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Leukemia stem cells (LSCs) that survive conventional chemotherapy are thought to contribute to disease relapse, leading to poor long-term outcomes for patients with acute myeloid leukemia (AML). We previously identified a Src-family kinase (SFK) member, hematopoietic cell kinase (HCK), as a molecular target that is highly differentially expressed in human primary LSCs compared with human normal hematopoietic stem cells (HSCs). We performed a large-scale chemical library screen that integrated a high-throughput enzyme inhibition assay, in silico binding prediction, and crystal structure determination and found a candidate HCK inhibitor, RK-20449, a pyrrolo-pyrimidine derivative with an enzymatic IC50 (half maximal inhibitory concentration) in the subnanomolar range. A crystal structure revealed that RK-20449 bound the activation pocket of HCK. In vivo administration of RK-20449 to nonobese diabetic (NOD)/severe combined immunodeficient (SCID)/IL2rg(null) mice engrafted with highly aggressive therapy-resistant AML significantly reduced human LSC and non-stem AML burden. By eliminating chemotherapy-resistant LSCs, RK-20449 may help to prevent relapse and lead to improved patient outcomes in AML.
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Affiliation(s)
- Yoriko Saito
- Laboratory for Human Disease Models, RIKEN Research Center for Allergy and Immunology, Yokohama, Kanagawa 230-0045, Japan
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19
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Arunesh GM, Shanthi E, Krishna MH, Sooriya Kumar J, Viswanadhan VN. Small molecule inhibitors of PIM1 kinase: July 2009 to February 2013 patent update. Expert Opin Ther Pat 2013; 24:5-17. [PMID: 24131033 DOI: 10.1517/13543776.2014.848196] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
INTRODUCTION The proviral insertion in murine (PIM) lymphoma proteins for which three isoforms, PIM1, PIM2 and PIM3 have been identified, belonging to the family of serine/threonine kinases has emerged recently as an important therapeutic target for the development of selective inhibitors as the new drugs for treating hematological malignancies and solid tumors. The small molecules developed by academia and the pharmaceutical industry have steadily increased in the last few years. Several drug discovery groups focus on treating disorders, such as cancer mediated by PIM kinase, have provided preclinical evidence suggesting that PIM inhibitor provides anti-apoptotic activity, inhibit cell survival and cell proliferation. AREAS COVERED This article discloses recent reviews on research and advances published in the patent literature and scientific publications from July 2009 to February 2013, highlighting discoveries on PIM1 kinase. EXPERT OPINION Several PIM1 kinase small molecule inhibitors are now at the pre-clinical research stage, development and testing. Though nearly 40 patents emerged in the last 3 years, greater efforts towards additional designs and medicinal chemistry continues for developing clinically efficacious PIM1 inhibitors, due to the significance of the target for cancer and the potential for novel and diverse inhibitors as drug candidates.
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Affiliation(s)
- Gubbi M Arunesh
- Department of Computational Chemistry and Informatics, Jubilant Biosys Ltd, Industrial Suburb , 96, Industrial Suburb, 2nd Stage, Yeshwanthpur, Bangalore 560 022, Karnataka , India +91 80 6662 8908 ; +91 80 66628333 ;
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20
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Ekambaram R, Enkvist E, Vaasa A, Kasari M, Raidaru G, Knapp S, Uri A. Selective bisubstrate inhibitors with sub-nanomolar affinity for protein kinase Pim-1. ChemMedChem 2013; 8:909-13. [PMID: 23616352 DOI: 10.1002/cmdc.201300042] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 04/05/2013] [Indexed: 11/06/2022]
Abstract
Potent and selective: The unique nature of the ATP binding pocket structure of Pim family protein kinases (PKs) was used for the development of bisubstrate inhibitors and a fluorescent probe with sub-nanomolar affinity. Conjugates of arginine-rich peptides with two ATP mimetic scaffolds were synthesized and tested as inhibitors of Pim-1. Against a panel of 124 protein kinases, a novel ARC-PIM conjugate selectively inhibited PKs of the Pim family.
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21
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Blanco-Aparicio C, Carnero A. Pim kinases in cancer: diagnostic, prognostic and treatment opportunities. Biochem Pharmacol 2012; 85:629-643. [PMID: 23041228 DOI: 10.1016/j.bcp.2012.09.018] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 09/18/2012] [Accepted: 09/18/2012] [Indexed: 12/14/2022]
Abstract
PIM proteins belong to a family of ser/thr kinases composed of 3 members, PIM1, PIM2 and PIM3, with greatly overlapping functions. PIM kinases are mainly responsible for cell cycle regulation, antiapoptotic activity and the homing and migration of receptor tyrosine kinases mediated via the JAK/STAT pathway. PIM kinases have been found to be upregulated in many hematological malignancies and solid tumors. Although these kinases have been described as weak oncogenes, they are heavily targeted for anticancer drug discovery. The present review summarizes the discoveries made to date regarding PIM kinases as driving oncogenes in the process of tumorigenesis and their validation as drug targets.
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Affiliation(s)
- Carmen Blanco-Aparicio
- Experimental Therapeutics Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Amancio Carnero
- Instituto de Biomedicina de Sevilla (IBiS), HUVR/CSIC/Universidad de Sevilla, Sevilla, Spain; Consejo Superior de Investigaciones Cientificas, Spain.
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22
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Ogawa N, Yuki H, Tanaka A. Insights from Pim1 structure for anti-cancer drug design. Expert Opin Drug Discov 2012; 7:1177-92. [DOI: 10.1517/17460441.2012.727394] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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23
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Parker LJ, Watanabe H, Tsuganezawa K, Tomabechi Y, Handa N, Shirouzu M, Yuki H, Honma T, Ogawa N, Nagano T, Yokoyama S, Tanaka A. Flexibility of the P-loop of Pim-1 kinase: observation of a novel conformation induced by interaction with an inhibitor. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:860-6. [PMID: 22869110 PMCID: PMC3412761 DOI: 10.1107/s1744309112027108] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 06/15/2012] [Indexed: 12/27/2022]
Abstract
The serine/threonine kinase Pim-1 is emerging as a promising target for cancer therapeutics. Much attention has recently been focused on identifying potential Pim-1 inhibitor candidates for the treatment of haematopoietic malignancies. The outcome of a rational drug-design project has recently been reported [Nakano et al. (2012), J. Med. Chem. 55, 5151-5156]. The report described the process of optimization of the structure-activity relationship and detailed from a medicinal chemistry perspective the development of a low-potency and nonselective compound initially identified from in silico screening into a potent, selective and metabolically stable Pim-1 inhibitor. Here, the structures of the initial in silico hits are reported and the noteworthy features of the Pim-1 complex structures are described. A particular focus was placed on the rearrangement of the glycine-rich P-loop region that was observed for one of the initial compounds, (Z)-7-(azepan-1-ylmethyl)-2-[(1H-indol-3-yl)methylidene]-6-hydroxy-1-benzofuran-3(2H)-one (compound 1), and was also found in all further derivatives. This novel P-loop conformation, which appears to be stabilized by an additional interaction with the β3 strand located above the binding site, is not usually observed in Pim-1 structures.
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Affiliation(s)
- Lorien J. Parker
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Hisami Watanabe
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Keiko Tsuganezawa
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Yuri Tomabechi
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Noriko Handa
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Mikako Shirouzu
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Hitomi Yuki
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Teruki Honma
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Naoko Ogawa
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Tetsuo Nagano
- Open Innovation Center for Drug Discovery, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Laboratory of Structural Biology, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akiko Tanaka
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Open Innovation Center for Drug Discovery, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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24
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Nakano H, Saito N, Parker L, Tada Y, Abe M, Tsuganezawa K, Yokoyama S, Tanaka A, Kojima H, Okabe T, Nagano T. Rational Evolution of a Novel Type of Potent and Selective Proviral Integration Site in Moloney Murine Leukemia Virus Kinase 1 (PIM1) Inhibitor from a Screening-Hit Compound. J Med Chem 2012; 55:5151-64. [DOI: 10.1021/jm3001289] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hirofumi Nakano
- Open Innovation Center for Drug
Discovery, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo
113-0033, Japan
| | - Nae Saito
- Open Innovation Center for Drug
Discovery, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo
113-0033, Japan
| | - Lorien Parker
- RIKEN Systems
and Structural
Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Yukio Tada
- Open Innovation Center for Drug
Discovery, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo
113-0033, Japan
| | - Masanao Abe
- Open Innovation Center for Drug
Discovery, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo
113-0033, Japan
| | - Keiko Tsuganezawa
- RIKEN Systems
and Structural
Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems
and Structural
Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Akiko Tanaka
- Open Innovation Center for Drug
Discovery, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo
113-0033, Japan
- RIKEN Systems
and Structural
Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Hirotatsu Kojima
- Open Innovation Center for Drug
Discovery, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo
113-0033, Japan
| | - Takayoshi Okabe
- Open Innovation Center for Drug
Discovery, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo
113-0033, Japan
| | - Tetsuo Nagano
- Open Innovation Center for Drug
Discovery, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo
113-0033, Japan
- Graduate School of Pharmaceutical
Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033,
Japan
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