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Sugita M, Onishi I, Irisa M, Yoshida N, Hirata F. Molecular Recognition and Self-Organization in Life Phenomena Studied by a Statistical Mechanics of Molecular Liquids, the RISM/3D-RISM Theory. Molecules 2021; 26:E271. [PMID: 33430461 PMCID: PMC7826681 DOI: 10.3390/molecules26020271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 11/18/2022] Open
Abstract
There are two molecular processes that are essential for living bodies to maintain their life: the molecular recognition, and the self-organization or self-assembly. Binding of a substrate by an enzyme is an example of the molecular recognition, while the protein folding is a good example of the self-organization process. The two processes are further governed by the other two physicochemical processes: solvation and the structural fluctuation. In the present article, the studies concerning the two molecular processes carried out by Hirata and his coworkers, based on the statistical mechanics of molecular liquids or the RISM/3D-RISM theory, are reviewed.
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Affiliation(s)
- Masatake Sugita
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-76, 2-12-1, Ookayama Meguro-ku, Tokyo 152-8550, Japan;
| | - Itaru Onishi
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan; (I.O.); (M.I.)
| | - Masayuki Irisa
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan; (I.O.); (M.I.)
| | - Norio Yoshida
- Department of Chemistry, Kyushu University, Fukuoka, Fukuoka 812-8581, Japan;
| | - Fumio Hirata
- Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
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2
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Barberis C, Erdman P, Czekaj M, Fire L, Pribish J, Tserlin E, Maniar S, Batchelor JD, Liu J, Patel VF, Hebert A, Levit M, Wang A, Sun F, Huang SMA. Discovery of SARxxxx92, a pan-PIM kinase inhibitor, efficacious in a KG1 tumor model. Bioorg Med Chem Lett 2020; 30:127625. [PMID: 33096160 DOI: 10.1016/j.bmcl.2020.127625] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/10/2020] [Accepted: 10/14/2020] [Indexed: 11/25/2022]
Abstract
N-substituted azaindoles were discovered as potent pan-PIM inhibitors. Lead optimization, guided by structure and focused on physico-chemical properties allowed us to solve inherent hERG and permeability liabilities, and provided compound 27, which subsequently impacted KG-1 tumor growth in a mouse model.
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Affiliation(s)
- Claude Barberis
- IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States.
| | - Paul Erdman
- IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States; Present address: AbbVie, 100 Abbott Park Road, Abbott Park, IL 60064-3500, United States
| | - Mark Czekaj
- IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States
| | - Luke Fire
- IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States; Present address: Rakuten Medical, 11080 Roselle St, San Diego, CA 92121, United States
| | - James Pribish
- IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States
| | - Elina Tserlin
- Present address: Qiagen, 561 Virginia Road, Concord, MA 01742, United States
| | - Sachin Maniar
- IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States
| | - Joseph D Batchelor
- IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States
| | - Jinyu Liu
- IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States
| | - Vinod F Patel
- Present address: TME Therapeutics, 3 Mossy Lane, Acton, MA 01720, United States
| | - Andrew Hebert
- Oncology Biochemistry, Sanofi, 270 Albany Street, Cambridge MA 02139, United States
| | - Mikhail Levit
- Oncology Biochemistry, Sanofi, 270 Albany Street, Cambridge MA 02139, United States
| | - Anlai Wang
- Oncology Biology, Sanofi, 270 Albany Street, Cambridge MA 02139, United States
| | - Frank Sun
- Oncology Pharmacology, Sanofi, 640 Memorial Drive, Cambridge MA 02139, United States
| | - Shih-Min A Huang
- Oncology Biology, Sanofi, 270 Albany Street, Cambridge MA 02139, United States; Present address: Bristol-Myers Squibb, 3551 Lawrenceville Princeton, Lawrence Township, NJ 08648, United States
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3
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Sergeev PG, Nenajdenko VG. Recent advances in the chemistry of pyridazine — an important representative of six-membered nitrogen heterocycles. RUSSIAN CHEMICAL REVIEWS 2020. [DOI: 10.1070/rcr4922] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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4
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Ashida T, Kikuchi T. A new method for estimating the relative binding free energy, derived from a free energy variational principle for the Pim-1-kinase-ligand and FKBP-ligand systems. J Comput Aided Mol Des 2020; 34:647-658. [PMID: 32107701 DOI: 10.1007/s10822-020-00302-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 02/14/2020] [Indexed: 11/26/2022]
Abstract
In this study, a new method is proposed for calculating the relative binding free energy between a ligand and a protein, derived from a free energy variational principle (FEVP). To address the shortcomings of the method used in our previous study, we incorporate the dynamical fluctuation of a ligand in the FEVP calculation. The present modified method is applied to the Pim-1-kinase-ligand system and also to the FKBP-ligand system as a comparison with our previous work. Any inhibitor of Pim-1 kinase is expected to function as an anti-cancer drug. Some improvements are observed in the results compared to the previous study. The present work also shows comparable or better results than approaches using a standard technique of binding free energy calculations, such as the LIE and the MM-PB/SA methods. The possibility of applying the present method in the drug discovery process is also discussed.
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Affiliation(s)
- Takeshi Ashida
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Takeshi Kikuchi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
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5
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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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6
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Discovery of novel triazolo[4,3-b]pyridazin-3-yl-quinoline derivatives as PIM inhibitors. Eur J Med Chem 2019; 168:87-109. [PMID: 30802730 DOI: 10.1016/j.ejmech.2019.02.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/24/2019] [Accepted: 02/07/2019] [Indexed: 11/22/2022]
Abstract
PIM kinase family (PIM-1, PIM-2 and PIM-3) is an appealing target for the discovery and development of selective inhibitors, useful in various disease conditions in which these proteins are highly expressed, such as cancer. The significant effort put, in the recent years, towards the development of small molecules exhibiting inhibitory activity against this protein family has ended up with several molecules entering clinical trials. As part of our ongoing exploration for potential drug candidates that exhibit affinity towards this protein family, we have generated a novel chemical series of triazolo[4,3-b]pyridazine based tricycles by applying a scaffold hopping strategy over our previously reported potent pan-PIM inhibitor ETP-47453 (compound 2). The structure-activity relationship studies presented herein demonstrate a rather selective PIM-1/PIM-3 biochemical profile for this novel series of tricycles, although pan-PIM and PIM-1 inhibitors have also been identified. Selected examples show significant inhibition of the phosphorylation of BAD protein in a cell-based assay. Moreover, optimized and highly selective compounds, such as 42, did not show significant hERG inhibition at 20 μM concentration, and proved its antiproliferative activity and utility in combination with particular antitumoral agents in several tumor cell lines.
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7
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Barberis C, Pribish J, Tserlin E, Gross A, Czekaj M, Barragué M, Erdman P, Maniar S, Jiang J, Fire L, Patel V, Hebert A, Levit M, Wang A, Sun F, Huang SMA. Discovery of N-substituted 7-azaindoles as Pan-PIM kinases inhibitors - Lead optimization - Part III. Bioorg Med Chem Lett 2019; 29:491-495. [PMID: 30553737 DOI: 10.1016/j.bmcl.2018.12.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 12/04/2018] [Accepted: 12/08/2018] [Indexed: 12/17/2022]
Abstract
N-substituted azaindoles were discovered as promising pan-PIM inhibitors. Lead optimization is described en route toward the identification of a clinical candidate. Modulation of physico-chemical properties allowed to solve inherent hERG and permeability liabilities. Compound 17 showed tumor growth inhibition in a KG1 tumor-bearing mouse model.
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Affiliation(s)
- Claude Barberis
- IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States.
| | - James Pribish
- IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States
| | - Elina Tserlin
- IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States
| | - Alexandre Gross
- IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States
| | - Mark Czekaj
- IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States
| | - Matthieu Barragué
- IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States
| | - Paul Erdman
- IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States
| | - Sachin Maniar
- IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States
| | - John Jiang
- IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States
| | - Luke Fire
- IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States
| | - Vinod Patel
- IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States
| | - Andrew Hebert
- Oncology Biochemistry, Sanofi, 270 Albany Street, Cambridge MA 02139, United States
| | - Mikhail Levit
- Oncology Biochemistry, Sanofi, 270 Albany Street, Cambridge MA 02139, United States
| | - Anlai Wang
- Oncology Biology, Sanofi, 270 Albany Street, Cambridge MA 02139, United States
| | - Frank Sun
- Oncology Pharmacology, Sanofi, 640 Memorial Drive, Cambridge MA 02139, United States
| | - Shih-Min A Huang
- Oncology Biology, Sanofi, 270 Albany Street, Cambridge MA 02139, United States
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8
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Hasegawa T, Sugita M, Kikuchi T, Hirata F. A Systematic Analysis of the Binding Affinity between the Pim-1 Kinase and Its Inhibitors Based on the MM/3D-RISM/KH Method. J Chem Inf Model 2017; 57:2789-2798. [PMID: 29019402 DOI: 10.1021/acs.jcim.7b00158] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A systematic study of the binding affinities of 16 lead compounds targeting the Pim-1 kinase based on the 3D-RISM/KH theory and MD simulations is reported. The results show a correlation coefficient R = 0.69 between the theoretical and experimental values of the binding free energy. This demonstrates that the method is applicable to the problem of compound screening and lead optimization, for which relative values of the free energy among the compounds have significance. We elucidate the contribution of the ligand fragments to the binding free energy. Our results indicate that the interactions between the residues and the triazolo[4,3-b]pyridazine scaffold as well as the phenyl ring of the ligand molecule make significant contributions to stabilization of the complex. Using the 3D-RISM/KH theory, we further analyze the probability distribution of a ligand fragment around the protein-ligand complex in which the substituent around the phenyl ring is removed from the ligand. The results demonstrate that the 3D-RISM/KH theory is capable of predicting the position of substitution on a ligand that has a higher affinity to a target protein.
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Affiliation(s)
- Takeshi Hasegawa
- Department of Bioinformatics, College of Life Science, Ritsumeikan University , 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Masatake Sugita
- Department of Bioinformatics, College of Life Science, Ritsumeikan University , 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Takeshi Kikuchi
- Department of Bioinformatics, College of Life Science, Ritsumeikan University , 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Fumio Hirata
- Toyota Physical and Chemical Research Institute , 41-1 Yokomichi, Nagakute, Aichi 480-1192, Japan
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9
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Kim C, Park MS. Synthesis and Evaluation of Novel 3-Allylseleno-6-Alkylsulfonylpyridazine Derivatives with Potential Anticancer Properties. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chaewon Kim
- College of Pharmacy; Duksung Women's University; Seoul 01369 Korea
| | - Myung-Sook Park
- College of Pharmacy; Duksung Women's University; Seoul 01369 Korea
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10
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Barberis C, Moorcroft N, Pribish J, Tserlin E, Gross A, Czekaj M, Barrague M, Erdman P, Majid T, Batchelor J, Levit M, Hebert A, Shen L, Moreno-Mazza S, Wang A. Discovery of N-substituted 7-azaindoles as Pan-PIM kinase inhibitors - Lead series identification - Part II. Bioorg Med Chem Lett 2017; 27:4735-4740. [PMID: 28927793 DOI: 10.1016/j.bmcl.2017.08.068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/25/2017] [Accepted: 08/31/2017] [Indexed: 02/08/2023]
Abstract
N-Substituted azaindoles have been discovered as pan-PIM kinase inhibitors. Initial SAR, early ADME and PK/PD data of a series of compounds is described and led to the identification of promising pan-PIM inhibitors which validated our interest in the 7-azaindole scaffold and led us to pursue the identification of a clinical candidate.
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Affiliation(s)
- Claude Barberis
- IDD Medicinal Chemistry, Sanofi Genzyme, 153 Second Avenue, Waltham, MA 02451, USA.
| | - Neil Moorcroft
- IDD Medicinal Chemistry, Sanofi Genzyme, 153 Second Avenue, Waltham, MA 02451, USA
| | - James Pribish
- IDD Medicinal Chemistry, Sanofi Genzyme, 153 Second Avenue, Waltham, MA 02451, USA
| | - Elina Tserlin
- IDD Medicinal Chemistry, Sanofi Genzyme, 153 Second Avenue, Waltham, MA 02451, USA
| | - Alexandre Gross
- IDD Medicinal Chemistry, Sanofi Genzyme, 153 Second Avenue, Waltham, MA 02451, USA
| | - Mark Czekaj
- IDD Medicinal Chemistry, Sanofi Genzyme, 153 Second Avenue, Waltham, MA 02451, USA
| | - Matthieu Barrague
- IDD Medicinal Chemistry, Sanofi Genzyme, 153 Second Avenue, Waltham, MA 02451, USA
| | - Paul Erdman
- IDD Medicinal Chemistry, Sanofi Genzyme, 153 Second Avenue, Waltham, MA 02451, USA
| | - Tahir Majid
- IDD Medicinal Chemistry, Sanofi Genzyme, 153 Second Avenue, Waltham, MA 02451, USA
| | - Joseph Batchelor
- IDD In Vitro Biology, Sanofi, 153 Second Avenue, Waltham, MA 02451, USA
| | - Mikhail Levit
- Oncology Biology, Sanofi, 270 Albany Street, Cambridge, MA 02139, USA
| | - Andrew Hebert
- Oncology Biology, Sanofi, 270 Albany Street, Cambridge, MA 02139, USA
| | - Liduo Shen
- DSAR, Sanofi Genzyme, 211 Second Avenue, Waltham, MA 02451, USA
| | | | - Anlai Wang
- Oncology Biology, Sanofi, 270 Albany Street, Cambridge, MA 02139, USA
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11
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Kim C, Kim SB, Jung J, Park MS. Design, Synthesis, and Biological Evaluation of Selenium-incorporated Aminopyridazines as Anticancer Agents. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10319] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Chaewon Kim
- College of Pharmacy; Duksung Women's University; Seoul 132-714 Korea
| | - Saet-Byeul Kim
- College of Pharmacy; Duksung Women's University; Seoul 132-714 Korea
| | - Joohee Jung
- College of Pharmacy; Duksung Women's University; Seoul 132-714 Korea
| | - Myung-Sook Park
- College of Pharmacy; Duksung Women's University; Seoul 132-714 Korea
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12
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Srinivasan R, Sembian Ruso J, Nagarajan NS, Senthil Kumaran R, Manickam G. A Convenient One-Pot Synthesis of Triazolopyridine and Related Heterocycle Fused-Triazole Analogs Through Copper Catalyzed Oxidative Cyclization Strategy. J Heterocycl Chem 2015. [DOI: 10.1002/jhet.2331] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- R. Srinivasan
- Department of Chemistry; Gandhigram Rural Institute - Deemed University; Gandhigram 624 302 Tamil Nadu India
- Syngene International Ltd; Bangalore 560099 India
| | - J. Sembian Ruso
- Department of Polymer Science; University of Madras; Maraimalai Campus, Guindy Chennai 600025 India
| | - N. S. Nagarajan
- Department of Chemistry; Gandhigram Rural Institute - Deemed University; Gandhigram 624 302 Tamil Nadu India
| | | | - G. Manickam
- Syngene International Ltd; Bangalore 560099 India
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13
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Wurz RP, Pettus LH, Jackson C, Wu B, Wang HL, Herberich B, Cee V, Lanman BA, Reed AB, Chavez F, Nixey T, Laszlo J, Wang P, Nguyen Y, Sastri C, Guerrero N, Winston J, Lipford JR, Lee MR, Andrews KL, Mohr C, Xu Y, Zhou Y, Reid DL, Tasker AS. The discovery and optimization of aminooxadiazoles as potent Pim kinase inhibitors. Bioorg Med Chem Lett 2015; 25:847-55. [DOI: 10.1016/j.bmcl.2014.12.067] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 12/16/2014] [Accepted: 12/19/2014] [Indexed: 11/26/2022]
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14
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Abstract
Pim oncogenes are highly expressed in many types of hematological and solid cancers. Pim kinases regulate the network of signaling pathways that are critical for tumorigenesis and development, making Pim kinases the attractive drug targets. Currently, two approaches have been employed in designing Pim kinase inhibitors: ATP-mimetics and non-ATP mimetics; but all target the ATP-binding pocket and are ATP-competitive. In this review, we summarize the current progress in understanding the Pim-related structure and biology, and provide insights into the binding modes of some prototypical Pim-1 inhibitors. The challenges as well as opportunities are highlighted for development of Pim kinase inhibitors as potential anticancer agents.
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15
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Rimaz M. Two Efficient One-Pot Approaches for Regioselective Synthesis of New 3-Arylpyridazino[4,3-c]quinolin-5(6H)-ones. Aust J Chem 2015. [DOI: 10.1071/ch15029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Two efficient regioselective approaches for the one-pot synthesis of 3-arylpyridazino[4,3-c]quinolin-5(6H)-one derivatives are reported, by the three-component reaction of arylglyoxal monohydrates, quinoline-2,4-diol, and hydrazinium dihydrochloride or hydrazine hydrate in ethanol and pyridine. In ethanol, the reactions were catalyzed by 1,4-diazobicyclo[2,2,2]octane. The features of both procedures are high regioselectivity, mild reaction conditions, good to high yields, and operational simplicity.
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16
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Discovery and identification of PIM-1 kinase inhibitors through a hybrid screening approach. Mol Divers 2014; 18:335-44. [DOI: 10.1007/s11030-014-9504-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 01/13/2014] [Indexed: 10/25/2022]
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17
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Kim C, Park EH, Park MS. Novel Alkylaminopyridazine Derivatives: Synthesis and Their Anti-proliferative Effects against MCF-7 Cells. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.11.3317] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Dwyer MP, Keertikar K, Paruch K, Alvarez C, Labroli M, Poker C, Fischmann TO, Mayer-Ezell R, Bond R, Wang Y, Azevedo R, Guzi TJ. Discovery of pyrazolo[1,5-a]pyrimidine-based Pim inhibitors: a template-based approach. Bioorg Med Chem Lett 2013; 23:6178-82. [PMID: 24091081 DOI: 10.1016/j.bmcl.2013.08.110] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 08/26/2013] [Accepted: 08/29/2013] [Indexed: 12/01/2022]
Abstract
The synthesis and hit-to-lead SAR development from a pyrazolo[1,5-a]pyrimidine-derived hit 5 to the identification of a series of potent, pan-Pim inhibitors such as 11j are described.
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Affiliation(s)
- Michael P Dwyer
- Department of Chemical Research, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, United States.
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19
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Lee SJ, Han BG, Cho JW, Choi JS, Lee J, Song HJ, Koh JS, Lee BI. Crystal structure of pim1 kinase in complex with a pyrido[4,3-d]pyrimidine derivative suggests a unique binding mode. PLoS One 2013; 8:e70358. [PMID: 23936194 PMCID: PMC3729456 DOI: 10.1371/journal.pone.0070358] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 06/18/2013] [Indexed: 02/07/2023] Open
Abstract
Human Pim1 kinase is a serine/threonine protein kinase that plays important biological roles in cell survival, apoptosis, proliferation, and differentiation. Moreover, Pim1 is up-regulated in various hematopoietic malignancies and solid tumors. Thus, Pim1 is an attractive target for cancer therapeutics, and there has been growing interest in developing small molecule inhibitors for Pim1. Here, we describe the crystal structure of Pim1 in complex with a newly developed pyrido[4,3-d]pyrimidine-derivative inhibitor (SKI-O-068). Our inhibitor exhibits a half maximum inhibitory concentration (IC50) of 123 (±14) nM and has an unusual binding mode in complex with Pim1 kinase. The interactions between SKI-O-068 and the Pim1 active site pocket residue are different from those of other scaffold inhibitor-bound structures. The binding mode analysis suggests that the SKI-O-068 inhibitor can be improved by introducing functional groups that facilitate direct interaction with Lys67, which aid in the design of an optimized inhibitor.
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Affiliation(s)
- Sang Jae Lee
- Biomolecular Function Research Branch, Research Institute, National Cancer Center, Goyang, Gyeonggi, Republic of Korea
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Byeong-Gu Han
- Biomolecular Function Research Branch, Research Institute, National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - Jea-Won Cho
- Biomolecular Function Research Branch, Research Institute, National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | | | - Jaekyoo Lee
- Genosco, Cambridge, Massachusetts, United States of America
| | - Ho-Juhn Song
- Genosco, Cambridge, Massachusetts, United States of America
| | - Jong Sung Koh
- Oscotec Inc., Seongnam, Gyeonggi, Republic of Korea
- Genosco, Cambridge, Massachusetts, United States of America
- * E-mail: (JSK); (BIL)
| | - Byung Il Lee
- Biomolecular Function Research Branch, Research Institute, National Cancer Center, Goyang, Gyeonggi, Republic of Korea
- * E-mail: (JSK); (BIL)
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20
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Bel Abed H, Mammoliti O, Bande O, Van Lommen G, Herdewijn P. Strategy for the synthesis of pyridazine heterocycles and their derivatives. J Org Chem 2013; 78:7845-58. [PMID: 23947534 DOI: 10.1021/jo400989q] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The first synthesis of novel fused pyridazines has been realized starting from 1,3-diketones involving a Diaza-Wittig reaction as a key step. A convenient strategy was elaborated to access versatile pyridazine derivatives allowing the variation of substituents at position 6 of the heterocyclic ring. In a first part, pyridazines bearing an ester group were synthesized as a model to evaluate the methodology. In a second part, an improved procedure has been used for the synthesis of pyridazines bearing a ketone group and different methods of cyclization were carried out, leading to several hitherto unknown biheterocyclic compounds. This reaction scheme represents an attractive methodology for the synthesis of novel fused pyridazine derivatives.
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Affiliation(s)
- Hassen Bel Abed
- Rega Institute for Medical Research, Laboratory of Medicinal Chemistry, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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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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Dakin LA, Block MH, Chen H, Code E, Dowling JE, Feng X, Ferguson AD, Green I, Hird AW, Howard T, Keeton EK, Lamb ML, Lyne PD, Pollard H, Read J, Wu AJ, Zhang T, Zheng X. Discovery of novel benzylidene-1,3-thiazolidine-2,4-diones as potent and selective inhibitors of the PIM-1, PIM-2, and PIM-3 protein kinases. Bioorg Med Chem Lett 2012; 22:4599-604. [PMID: 22727640 DOI: 10.1016/j.bmcl.2012.05.098] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 05/18/2012] [Accepted: 05/29/2012] [Indexed: 12/22/2022]
Abstract
Novel substituted benzylidene-1,3-thiazolidine-2,4-diones (TZDs) have been identified as potent and highly selective inhibitors of the PIM kinases. The synthesis and SAR of these compounds are described, along with X-ray crystallographic, anti-proliferative, and selectivity data.
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Affiliation(s)
- Les A Dakin
- Oncology iMed Sciences Group, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
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24
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The design, synthesis, and biological evaluation of PIM kinase inhibitors. Bioorg Med Chem Lett 2012; 22:3732-8. [PMID: 22542012 DOI: 10.1016/j.bmcl.2012.04.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 03/22/2012] [Accepted: 04/03/2012] [Indexed: 11/23/2022]
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25
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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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26
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Abstract
INTRODUCTION Inhibition of protein kinases has become a standard of modern clinical oncology. PIM1 belongs to a novel class of serine/threonine kinases with distinct molecular and biochemical features regulating various oncogenic pathways, for example hypoxia response, cell cycle progression and apoptosis resistance. PIM1 is overexpressed in human cancer diseases and has been associated with metastasis and overall treatment response; in experimental models, inhibition of PIM1 suppressed cell proliferation and migration, induced apoptotic cell death and synergized with other chemotherapeutic agents. AREAS COVERED A PubMed literature search was performed to review the currently available data on PIM1 expression, regulation and targets; its implication in different types of cancer and its impact on prognosis are described. We present ATP-competitive PIM1 inhibitors and the state of the art of PIM1 inhibitor design. Finally, we highlight the development of the unusual class of highly selective and potent organometallic PIM1 inhibitors. EXPERT OPINION As PIM1 possesses oncogenic functions and is overexpressed in various kinds of cancer diseases, its inhibition provides a new option in cancer therapy. Based on the ability of highly selective organometallic PIM1 inhibitors, promising in vivo applicability is expected.
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Affiliation(s)
- Anna Lena Merkel
- Philipps University Marburg, Institute for Surgical Research, Baldingerstrasse, Marburg, 35033, Germany
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27
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Haddach M, Michaux J, Schwaebe MK, Pierre F, O’Brien SE, Borsan C, Tran J, Raffaele N, Ravula S, Drygin D, Siddiqui-Jain A, Darjania L, Stansfield R, Proffitt C, Macalino D, Streiner N, Bliesath J, Omori M, Whitten JP, Anderes K, Rice WG, Ryckman DM. Discovery of CX-6258. A Potent, Selective, and Orally Efficacious pan-Pim Kinases Inhibitor. ACS Med Chem Lett 2012; 3:135-9. [PMID: 24900437 DOI: 10.1021/ml200259q] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 12/27/2011] [Indexed: 11/30/2022] Open
Abstract
Structure-activity relationship analysis in a series of 3-(5-((2-oxoindolin-3-ylidene)methyl)furan-2-yl)amides identified compound 13, a pan-Pim kinases inhibitor with excellent biochemical potency and kinase selectivity. Compound 13 exhibited in vitro synergy with chemotherapeutics and robust in vivo efficacy in two Pim kinases driven tumor models.
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Affiliation(s)
- Mustapha Haddach
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - Jerome Michaux
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - Michael K. Schwaebe
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - Fabrice Pierre
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - Sean E. O’Brien
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - Cosmin Borsan
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - Joe Tran
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - Nicholas Raffaele
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - Suchitra Ravula
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - Denis Drygin
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - Adam Siddiqui-Jain
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - Levan Darjania
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - Ryan Stansfield
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - Chris Proffitt
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - Diwata Macalino
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - Nicole Streiner
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - Joshua Bliesath
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - May Omori
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - Jeffrey P. Whitten
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - Kenna Anderes
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - William G. Rice
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
| | - David M. Ryckman
- Cylene Pharmaceuticals Inc., 5820 Nancy
Ridge Drive, Suite 200, San Diego, California 92121,
United States
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28
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Abstract
The PIM genes represent a family of proto-oncogenes that encode three different serine/threonine protein kinases (PIM1, PIM2 and PIM3) with essential roles in the regulation of signal transduction cascades, which promote cell survival, proliferation and drug resistance. PIM kinases are overexpressed in several hematopoietic tumors and support in vitro and in vivo malignant cell growth and survival, through cell cycle regulation and inhibition of apoptosis. PIM kinases do not have an identified regulatory domain, which means that these proteins are constitutively active once transcribed. They appear to be critical downstream effectors of important oncoproteins and, when overexpressed, can mediate drug resistance to available agents, such as rapamycin. Recent crystallography studies reveal that, unlike other kinases, they possess a hinge region, which creates a unique binding pocket for ATP, offering a target for an increasing number of potent small-molecule PIM kinase inhibitors. Preclinical studies in models of various hematologic cancers indicate that these novel agents show promising activity and some of them are currently being evaluated in a clinical setting. In this review, we profile the PIM kinases as targets for therapeutics in hematologic malignancies.
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Affiliation(s)
- Yesid Alvarado
- Department of Hematology/Oncology, Cancer Therapy & Research Center, The University of Texas Health Science Center San Antonio, 7979 Wurzbach Road, MC8232, San Antonio, 78229, TX, USA
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29
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Pastor J, Oyarzabal J, Saluste G, Alvarez RM, Rivero V, Ramos F, Cendón E, Blanco-Aparicio C, Ajenjo N, Cebriá A, Albarrán M, Cebrián D, Corrionero A, Fominaya J, Montoya G, Mazzorana M. Hit to lead evaluation of 1,2,3-triazolo[4,5-b]pyridines as PIM kinase inhibitors. Bioorg Med Chem Lett 2012; 22:1591-7. [DOI: 10.1016/j.bmcl.2011.12.130] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 12/27/2011] [Accepted: 12/28/2011] [Indexed: 10/14/2022]
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30
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Abstract
Abstract
PIM serine/threonine kinases are overexpressed, translocated, or amplified in multiple B-cell lymphoma types. We have explored the frequency and relevance of PIM expression in different B-cell lymphoma types and investigated whether PIM inhibition could be a rational therapeutic approach. Increased expression of PIM2 was detected in subsets of mantle cell lymphoma, diffuse large B-cell lymphoma (DLBLC), follicular lymphoma, marginal zone lymphoma-mucosa–associated lymphoid tissue type, chronic lymphocytic leukemia, and nodal marginal zone lymphoma cases. Increased PIM2 protein expression was associated with an aggressive clinical course in activated B-like-DLBCL patients. Pharmacologic and genetic inhibition of PIM2 revealed p4E-BP1(Thr37/46) and p4E-BP1(Ser65) as molecular biomarkers characteristic of PIM2 activity and indicated the involvement of PIM2 kinase in regulating mammalian target of rapamycin complex 1. The simultaneous genetic inhibition of all 3 PIM kinases induced changes in apoptosis and cell cycle. In conclusion, we show that PIM2 kinase inhibition is a rational approach in DLBCL treatment, identify appropriate biomarkers for pharmacodynamic studies, and provide a new marker for patient stratification.
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31
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7-(4H-1,2,4-Triazol-3-yl)benzo[c][2,6]naphthyridines: A novel class of Pim kinase inhibitors with potent cell antiproliferative activity. Bioorg Med Chem Lett 2011; 21:6687-92. [DOI: 10.1016/j.bmcl.2011.09.059] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 09/14/2011] [Accepted: 09/15/2011] [Indexed: 11/21/2022]
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32
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Abstract
Studies of epilepsy have mainly focused on the membrane proteins that control neuronal excitability. Recently, attention has been shifting to intracellular proteins and their interactions, signaling cascades and feedback regulation as they relate to epilepsy. The mTOR (mammalian target of rapamycin) signal transduction pathway, especially, has been suggested to play an important role in this regard. These pathways are involved in major physiological processes as well as in numerous pathological conditions. Here, involvement of the mTOR pathway in epilepsy will be reviewed by presenting; an overview of the pathway, a brief description of key signaling molecules, a summary of independent reports and possible implications of abnormalities of those molecules in epilepsy, a discussion of the lack of experimental data, and questions raised for the understanding its epileptogenic mechanism.
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Affiliation(s)
- Chang Hoon Cho
- Epilepsy Research Laboratory Department of Pediatrics Children's Hospital of Philadelphia, Pennsylvania 19104, USA.
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33
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Nishiguchi GA, Atallah G, Bellamacina C, Burger MT, Ding Y, Feucht PH, Garcia PD, Han W, Klivansky L, Lindvall M. Discovery of novel 3,5-disubstituted indole derivatives as potent inhibitors of Pim-1, Pim-2, and Pim-3 protein kinases. Bioorg Med Chem Lett 2011; 21:6366-9. [PMID: 21945284 DOI: 10.1016/j.bmcl.2011.08.105] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 08/19/2011] [Accepted: 08/25/2011] [Indexed: 12/14/2022]
Abstract
A series of novel 3,5-disubstituted indole derivatives as potent and selective inhibitors of all three members of the Pim kinase family is described. High throughput screen identified a pan-Pim kinase inhibitor with a promiscuous scaffold. Guided by structure-based drug design, SAR of the series afforded a highly selective indole chemotype that was further developed into a potent set of compounds against Pim-1, 2, and 3 (Pim-1 and Pim-3: IC(50)≤2nM and Pim-2: IC(50)≤100nM).
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Affiliation(s)
- Gisele A Nishiguchi
- Global Discovery Chemistry/Oncology and Exploratory Chemistry, Novartis Institutes of BioMedical Research, Emeryville, CA 94608, USA.
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34
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Rapp C, Kalyanaraman C, Schiffmiller A, Schoenbrun EL, Jacobson MP. A molecular mechanics approach to modeling protein-ligand interactions: relative binding affinities in congeneric series. J Chem Inf Model 2011; 51:2082-9. [PMID: 21780805 DOI: 10.1021/ci200033n] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We introduce the "Prime-ligand" method for ranking ligands in congeneric series. The method employs a single scoring function, the OPLS-AA/GBSA molecular mechanics/implicit solvent model, for all stages of sampling and scoring. We evaluate the method using 12 test sets of congeneric series for which experimental binding data is available in the literature, as well as the structure of one member of the series bound to the protein. Ligands are "docked" by superimposing a common stem fragment among the compounds in the series using a crystal complex from the Protein Data Bank and sampling the conformational space of the variable region. Our results show good correlation between our predicted rankings and the experimental data for cases in which binding affinities differ by at least 1 order of magnitude. For 11 out of 12 cases, >90% of such ligand pairs could be correctly ranked, while for the remaining case, Factor Xa, 76% of such pairs were correctly ranked. A small number of compounds could not be docked using the current protocol because of the large size of functional groups that could not be accommodated by a rigid receptor. CPU requirements for the method, involving CPU minutes per ligand, are modest compared with more rigorous methods that use similar force fields, such as free energy perturbation. We also benchmark the scoring function using series of ligands bound to the same protein within the CSAR data set. We demonstrate that energy minimization of ligands in the crystal structures is critical to obtain any correlation with experimentally determined binding affinities.
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Affiliation(s)
- Chaya Rapp
- Department of Chemistry, Stern College for Women, Yeshiva University, New York, New York, United States
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35
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Isaac M, Siu A, Jongstra J. The oncogenic PIM kinase family regulates drug resistance through multiple mechanisms. Drug Resist Updat 2011; 14:203-11. [DOI: 10.1016/j.drup.2011.04.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 04/18/2011] [Accepted: 04/18/2011] [Indexed: 01/05/2023]
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36
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Ren JX, Li LL, Zheng RL, Xie HZ, Cao ZX, Feng S, Pan YL, Chen X, Wei YQ, Yang SY. Discovery of novel Pim-1 kinase inhibitors by a hierarchical multistage virtual screening approach based on SVM model, pharmacophore, and molecular docking. J Chem Inf Model 2011; 51:1364-75. [PMID: 21618971 DOI: 10.1021/ci100464b] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In this investigation, we describe the discovery of novel potent Pim-1 inhibitors by employing a proposed hierarchical multistage virtual screening (VS) approach, which is based on support vector machine-based (SVM-based VS or SB-VS), pharmacophore-based VS (PB-VS), and docking-based VS (DB-VS) methods. In this approach, the three VS methods are applied in an increasing order of complexity so that the first filter (SB-VS) is fast and simple, while successive ones (PB-VS and DB-VS) are more time-consuming but are applied only to a small subset of the entire database. Evaluation of this approach indicates that it can be used to screen a large chemical library rapidly with a high hit rate and a high enrichment factor. This approach was then applied to screen several large chemical libraries, including PubChem, Specs, and Enamine as well as an in-house database. From the final hits, 47 compounds were selected for further in vitro Pim-1 inhibitory assay, and 15 compounds show nanomolar level or low micromolar inhibition potency against Pim-1. In particular, four of them were found to have new scaffolds which have potential for the chemical development of Pim-1 inhibitors.
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Affiliation(s)
- Ji-Xia Ren
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
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37
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Xiang Y, Hirth B, Asmussen G, Biemann HP, Bishop KA, Good A, Fitzgerald M, Gladysheva T, Jain A, Jancsics K, Liu J, Metz M, Papoulis A, Skerlj R, Stepp JD, Wei RR. The discovery of novel benzofuran-2-carboxylic acids as potent Pim-1 inhibitors. Bioorg Med Chem Lett 2011; 21:3050-6. [DOI: 10.1016/j.bmcl.2011.03.030] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 03/07/2011] [Accepted: 03/09/2011] [Indexed: 11/27/2022]
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38
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Kozhevnikov DN, Prokhorov AM. Triazines, Tetrazines and Fused Ring Polyaza Systems. PROGRESS IN HETEROCYCLIC CHEMISTRY 2011. [DOI: 10.1016/s0959-6380(11)22014-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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39
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Abstract
The serine/threonine Pim kinases are overexpressed in solid cancers and hematologic malignancies and promote cell growth and survival. Here, we find that a novel Pim kinase inhibitor, SMI-4a, or Pim-1 siRNA blocked the rapamycin-sensitive mammalian target of rapamycin (mTORC1) activity by stimulating the phosphorylation and thus activating the mTORC1 negative regulator AMP-dependent protein kinase (AMPK). Mouse embryonic fibroblasts (MEFs) deficient for all three Pim kinases [triple knockout (TKO) MEFs] demonstrated activated AMPK driven by elevated ratios of AMPATP relative to wild-type MEFs. Consistent with these findings, TKO MEFs were found to grow slowly in culture and have decreased rates of protein synthesis secondary to a diminished amount of 5'-cap-dependent translation. Pim-3 expression alone in TKO MEFs was sufficient to reverse AMPK activation, increase protein synthesis, and drive MEF growth similar to wild type. Pim-3 expression was found to markedly increase the protein levels of both c-Myc and the peroxisome proliferator-activated receptor gamma coactivator 1α (PGC-1α), enzymes capable of regulating glycolysis and mitochondrial biogenesis, which were diminished in TKO MEFs. Overexpression of PGC-1α in TKO MEFs elevated ATP levels and inhibited the activation of AMPK. These results demonstrate the Pim kinase-mediated control of energy metabolism and thus regulation of AMPK activity. We identify an important role for Pim-3 in modulating c-Myc and PGC-1α protein levels and cell growth.
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40
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Akué-Gédu R, Nauton L, Théry V, Bain J, Cohen P, Anizon F, Moreau P. Synthesis, Pim kinase inhibitory potencies and in vitro antiproliferative activities of diversely substituted pyrrolo[2,3-a]carbazoles. Bioorg Med Chem 2010; 18:6865-73. [DOI: 10.1016/j.bmc.2010.07.036] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Revised: 05/26/2010] [Accepted: 07/15/2010] [Indexed: 10/19/2022]
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41
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Sliman F, Blairvacq M, Durieu E, Meijer L, Rodrigo J, Desmaële D. Identification and structure–activity relationship of 8-hydroxy-quinoline-7-carboxylic acid derivatives as inhibitors of Pim-1 kinase. Bioorg Med Chem Lett 2010; 20:2801-5. [DOI: 10.1016/j.bmcl.2010.03.061] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 03/11/2010] [Accepted: 03/12/2010] [Indexed: 11/29/2022]
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42
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Brault L, Gasser C, Bracher F, Huber K, Knapp S, Schwaller J. PIM serine/threonine kinases in the pathogenesis and therapy of hematologic malignancies and solid cancers. Haematologica 2010; 95:1004-15. [PMID: 20145274 DOI: 10.3324/haematol.2009.017079] [Citation(s) in RCA: 285] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The identification as cooperating targets of Proviral Integrations of Moloney virus in murine lymphomas suggested early on that PIM serine/threonine kinases play an important role in cancer biology. Whereas elevated levels of PIM1 and PIM2 were mostly found in hematologic malignancies and prostate cancer, increased PIM3 expression was observed in different solid tumors. PIM kinases are constitutively active and their activity supports in vitro and in vivo tumor cell growth and survival through modification of an increasing number of common as well as isoform-specific substrates including several cell cycle regulators and apoptosis mediators. PIM1 but not PIM2 seems also to mediate homing and migration of normal and malignant hematopoietic cells by regulating chemokine receptor surface expression. Knockdown experiments by RNA interference or dominant-negative acting mutants suggested that PIM kinases are important for maintenance of a transformed phenotype and therefore potential therapeutic targets. Determination of the protein structure facilitated identification of an increasing number of potent small molecule PIM kinase inhibitors with in vitro and in vivo anticancer activity. Ongoing efforts aim to identify isoform-specific PIM inhibitors that would not only help to dissect the kinase function but hopefully also provide targeted therapeutics. Here, we summarize the current knowledge about the role of PIM serine/threonine kinases for the pathogenesis and therapy of hematologic malignancies and solid cancers, and we highlight structural principles and recent progress on small molecule PIM kinase inhibitors that are on their way into first clinical trials.
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Affiliation(s)
- Laurent Brault
- Department of Biomedicine, University Hospital Basel, Hebelstrasse 20, 4031 Basel, Switzerland
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Lee KJ, Choi JK, Yum EK, Cho SY. Novel 1,3-dipolar cycloadditions of fulvenes and hydrazonyl chlorides: a facile synthesis of the cyclopenta[d]pyridazines. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.09.086] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Akué-Gédu R, Rossignol E, Azzaro S, Knapp S, Filippakopoulos P, Bullock AN, Bain J, Cohen P, Prudhomme M, Anizon F, Moreau P. Synthesis, kinase inhibitory potencies, and in vitro antiproliferative evaluation of new Pim kinase inhibitors. J Med Chem 2009; 52:6369-81. [PMID: 19788246 DOI: 10.1021/jm901018f] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Members of the Pim kinase family have been identified as promising targets for the development of antitumor agents. After a screening of pyrrolo[2,3-a]- and [3,2-a]carbazole derivatives toward 66 protein kinases, we identified pyrrolo[2,3-a]carbazole as a new scaffold to design potent Pim kinase inhibitors. In particular, compound 9 was identified as a low nM selective Pim inhibitor. Additionally, several pyrrolo[2,3-a]carbazole derivatives showed selectivity for Pim-1 and Pim-3 over Pim-2. In vitro antiproliferative activities of 9 and 28, the most potent Pim inhibitors identified, were evaluated toward three human solid cancer cell lines (PA1, PC3, and DU145) and one human fibroblast primary culture, revealing IC50 values in the micromolar range. Finally, the crystal structure of Pim-1 complexed with lead compound 9 was determined. The structure revealed a non-ATP mimetic binding mode with no hydrogen bonds formed with the kinase hinge region and explained the selectivity of pyrrolo[2,3-a]carbazole derivatives for Pim kinases.
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Affiliation(s)
- Rufine Akué-Gédu
- Clermont Université, Université Blaise Pascal, Laboratoire SEESIB, F-63177 Aubière, France
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