1
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Walhekar V, Bagul C, Kumar D, Muthal A, Achaiah G, Kulkarni R. Topical advances in PIM kinases and their inhibitors: Medicinal chemistry perspectives. Biochim Biophys Acta Rev Cancer 2022; 1877:188725. [DOI: 10.1016/j.bbcan.2022.188725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 12/28/2022]
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2
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Sobeh MM, Kitao A. Dissociation Pathways of the p53 DNA Binding Domain from DNA and Critical Roles of Key Residues Elucidated by dPaCS-MD/MSM. J Chem Inf Model 2022; 62:1294-1307. [PMID: 35234033 DOI: 10.1021/acs.jcim.1c01508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
p53 is a transcriptional factor that regulates cell response to a variety of stresses. About a half of all human tumors contain p53 mutations, and the accumulation of mutations in the DNA binding domain of p53 (p53-DBD) can cause destabilization of p53 and its complex with DNA. To identify the key residues of the p53-DBD/DNA binding and to understand the dissociation mechanisms of the p53-DBD/DNA complex, the dissociation process of p53-DBD from a DNA duplex that contains the consensus sequence (the specific target of p53-DBD) was investigated by a combination of dissociation parallel cascade selection molecular dynamics (dPaCS-MD) and the Markov state model (MSM). This combination (dPaCS-MD/MSM) enabled us to simulate dissociation of the two large molecules based on an all-atom model with a short simulation time (11.2 ± 2.2 ns per trial) and to analyze dissociation pathways, free energy landscape (FEL), and binding free energy. Among 75 trials of dPaCS-MD, p53-DBD dissociated first from the major groove and then detached from the minor groove in 93% of the cases, while 7% of the cases unbinding from the minor groove occurred first. Minor groove binding is mainly stabilized by R248, identified as the most important residue that tightly binds deep inside the minor groove. The standard binding free energy calculated from the FEL was -10.9 ± 0.4 kcal/mol, which agrees with an experimental value of -11.1 kcal/mol. These results indicate that the dPaCS-MD/MSM combination can be a powerful tool to investigate dissociation mechanisms of two large molecules. Analysis of the p53 key residues for DNA binding indicates high correlations with cancer-related mutations, confirming that impairment of the interactions between p53-DBD and DNA can be frequently related to cancer.
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Affiliation(s)
- Mohamed Marzouk Sobeh
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Physics Department, Faculty of Science, Ain Shams University, Cairo 11566, Egypt
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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3
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Hata H, Phuoc Tran D, Marzouk Sobeh M, Kitao A. Binding free energy of protein/ligand complexes calculated using dissociation Parallel Cascade Selection Molecular Dynamics and Markov state model. Biophys Physicobiol 2022; 18:305-316. [PMID: 35178333 PMCID: PMC8694779 DOI: 10.2142/biophysico.bppb-v18.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/02/2021] [Indexed: 01/01/2023] Open
Abstract
We recently proposed a computational procedure to simulate the dissociation of protein/ligand complexes using the dissociation Parallel Cascade Selection Molecular Dynamics simulation (dPaCS-MD) method and to analyze the generated trajectories using the Markov state model (MSM). This procedure, called dPaCS-MD/MSM, enables calculation of the dissociation free energy profile and the standard binding free energy. To examine whether this method can reproduce experimentally determined binding free energies for a variety of systems, we used it to investigate the dissociation of three protein/ligand complexes: trypsin/benzamine, FKBP/FK506, and adenosine A2A receptor/T4E. First, dPaCS-MD generated multiple dissociation pathways within a reasonable computational time for all the complexes, although the complexes differed significantly in the size of the molecules and in intermolecular interactions. Subsequent MSM analyses produced free energy profiles for the dissociations, which provided insights into how each ligand dissociates from the protein. The standard binding free energies obtained by dPaCS-MD/MSM are in good agreement with experimental values for all the complexes. We conclude that dPaCS-MD/MSM can accurately calculate the binding free energies of these complexes.
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Affiliation(s)
- Hiroaki Hata
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Duy Phuoc Tran
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Mohamed Marzouk Sobeh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.,Physics Department, Faculty of Science, Ain Shams University, Cairo 11566, Egypt
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
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4
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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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5
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Volynets GP, Pletnova LV, Sapelkin VM, Savytskyi OV, Yarmoluk SM. A computational analysis of the binding free energies of apoptosis signal-regulating kinase 1 inhibitors from different chemotypes. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1922686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Galyna P. Volynets
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, NAS of Ukraine, Kyiv, Ukraine
- Scientific Services Company Otava Ltd., Kyiv, Ukraine
| | - Larysa V. Pletnova
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, NAS of Ukraine, Kyiv, Ukraine
| | - Vladislav M. Sapelkin
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, NAS of Ukraine, Kyiv, Ukraine
| | - Oleksandr V. Savytskyi
- Department of Protein Engineering and Bioinformatics, Institute of Molecular Biology and Genetics, NAS of Ukraine, Kyiv, Ukraine
| | - Sergiy M. Yarmoluk
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, NAS of Ukraine, Kyiv, Ukraine
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6
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Rathi A, Kumar D, Hasan GM, Haque MM, Hassan MI. Therapeutic targeting of PIM KINASE signaling in cancer therapy: Structural and clinical prospects. Biochim Biophys Acta Gen Subj 2021; 1865:129995. [PMID: 34455019 DOI: 10.1016/j.bbagen.2021.129995] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/28/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND PIM kinases are well-studied drug targets for cancer, belonging to Serine/Threonine kinases family. They are the downstream target of various signaling pathways, and their up/down-regulation affects various physiological processes. PIM family comprises three isoforms, namely, PIM-1, PIM-2, and PIM-3, on alternative initiation of translation and they have different levels of expression in different types of cancers. Its structure shows a unique ATP-binding site in the hinge region which makes it unique among other kinases. SCOPE OF REVIEW PIM kinases are widely reported in hematological malignancies along with prostate and breast cancers. Currently, many drugs are used as inhibitors of PIM kinases. In this review, we highlighted the physiological significance of PIM kinases in the context of disease progression and therapeutic targeting. We comprehensively reviewed the PIM kinases in terms of their expression and regulation of different physiological roles. We further predicted functional partners of PIM kinases to elucidate their role in the cellular physiology of different cancer and mapped their interaction network. MAJOR CONCLUSIONS A deeper mechanistic insight into the PIM signaling involved in regulating different cellular processes, including transcription, apoptosis, cell cycle regulation, cell proliferation, cell migration and senescence, is provided. Furthermore, structural features of PIM have been dissected to understand the mechanism of inhibition and subsequent implication of designed inhibitors towards therapeutic management of prostate, breast and other cancers. GENERAL SIGNIFICANCE Being a potential drug target for cancer therapy, available drugs and PIM inhibitors at different stages of clinical trials are discussed in detail.
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Affiliation(s)
- Aanchal Rathi
- Department of Biotechnology, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Dhiraj Kumar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia
| | | | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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7
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Zheng Z, Borbulevych OY, Liu H, Deng J, Martin RI, Westerhoff LM. MovableType Software for Fast Free Energy-Based Virtual Screening: Protocol Development, Deployment, Validation, and Assessment. J Chem Inf Model 2020; 60:5437-5456. [PMID: 32791826 PMCID: PMC7781189 DOI: 10.1021/acs.jcim.0c00618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
For decades, the
complicated energy surfaces found in macromolecular
protein:ligand structures, which require large amounts of computational
time and resources for energy state sampling, have been an inherent
obstacle to fast, routine free energy estimation in industrial drug
discovery efforts. Beginning in 2013, the Merz research group addressed
this cost with the introduction of a novel sampling methodology termed
“Movable Type” (MT). Using numerical integration methods,
the MT method reduces the computational expense for energy state sampling
by independently calculating each atomic partition function from an
initial molecular conformation in order to estimate the molecular
free energy using ensembles of the atomic partition functions. In
this work, we report a software package, the DivCon Discovery Suite
with the MovableType module from QuantumBio Inc., that performs this
MT free energy estimation protocol in a fast, fully encapsulated manner.
We discuss the computational procedures and improvements to the original
work, and we detail the corresponding settings for this software package.
Finally, we introduce two validation benchmarks to evaluate the overall
robustness of the method against a broad range of protein:ligand structural
cases. With these publicly available benchmarks, we show that the
method can use a variety of input types and parameters and exhibits
comparable predictability whether the method is presented with “expensive”
X-ray structures or “inexpensively docked” theoretical
models. We also explore some next steps for the method. The MovableType
software is available at http://www.quantumbioinc.com/
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Affiliation(s)
- Zheng Zheng
- QuantumBio Inc., 2790 West College Avenue, Suite 900, State College, Pennsylvania 16801, United States.,School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Oleg Y Borbulevych
- QuantumBio Inc., 2790 West College Avenue, Suite 900, State College, Pennsylvania 16801, United States
| | - Hao Liu
- School of Mechanical and Electronic Engineering, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Jianpeng Deng
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Roger I Martin
- QuantumBio Inc., 2790 West College Avenue, Suite 900, State College, Pennsylvania 16801, United States
| | - Lance M Westerhoff
- QuantumBio Inc., 2790 West College Avenue, Suite 900, State College, Pennsylvania 16801, United States
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8
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Wang Z, Wang X, Kang Y, Zhong H, Shen C, Yao X, Cao D, Hou T. Binding affinity and dissociation pathway predictions for a series of USP7 inhibitors with pyrimidinone scaffold by multiple computational methods. Phys Chem Chem Phys 2020; 22:5487-5499. [DOI: 10.1039/d0cp00370k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ubiquitin specific protease 7 (USP7) has attracted increasing attention because of its multifaceted roles in different tumor types.
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Affiliation(s)
- Zhe Wang
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- Zhejiang 310058
- China
| | - Xuwen Wang
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- Zhejiang 310058
- China
| | - Yu Kang
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- Zhejiang 310058
- China
| | - Haiyang Zhong
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- Zhejiang 310058
- China
| | - Chao Shen
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- Zhejiang 310058
- China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine
- Macau Institute for Applied Research in Medicine and Health
- Macau University of Science and Technology
- Taipa
- China
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences
- Central South University
- Changsha 410013
- P. R. China
| | - Tingjun Hou
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- Zhejiang 310058
- China
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9
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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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10
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Tran DP, Kitao A. Dissociation Process of a MDM2/p53 Complex Investigated by Parallel Cascade Selection Molecular Dynamics and the Markov State Model. J Phys Chem B 2019; 123:2469-2478. [PMID: 30645121 DOI: 10.1021/acs.jpcb.8b10309] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Recently, we efficiently generated dissociation pathways of a protein-ligand complex without applying force bias with parallel cascade selection molecular dynamics (PaCS-MD) and showed that PaCS-MD in combination with the Markov state model (MSM) yielded a binding free energy comparable to experimental values. In this work, we applied the same procedure to a complex of MDM2 protein and the transactivation domain of p53 protein (TAD-p53), the latter of which is known to be very flexible in the unbound state. Using 30 independent MD simulations in PaCS-MD, we successfully generated 25 dissociation pathways of the complex, which showed complete or partial unfolding of the helical region of TAD-p53 during the dissociation process within an average simulation time of 154.8 ± 46.4 ns. The standard binding free energy obtained in combination with one-dimensional-, three-dimensional (3D)- or Cα-MSM was in good agreement with those determined experimentally. Using 3D-MSM based on the center of mass position of TAD-p53 relative to MDM2, the dissociation rate constant was calculated, which was comparable to those measured experimentally. Cα-MSM based on all Cα coordinates of TAD-p53 reproduced the experimentally measured standard binding free energy, and dissociation and association rate constants. We conclude that the combination of PaCS-MD and MSM offers an efficient computational procedure to calculate binding free energies and kinetic rates.
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Affiliation(s)
- Duy Phuoc Tran
- School of Life Sciences and Technology , Tokyo Institute of Technology , 2-12-1, Ookayama , Meguro-ku, Tokyo 152-8550 , Japan
| | - Akio Kitao
- School of Life Sciences and Technology , Tokyo Institute of Technology , 2-12-1, Ookayama , Meguro-ku, Tokyo 152-8550 , Japan
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11
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Structural analysis of PIM1 kinase complexes with ATP-competitive inhibitors. Sci Rep 2017; 7:13399. [PMID: 29042609 PMCID: PMC5645348 DOI: 10.1038/s41598-017-13557-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/25/2017] [Indexed: 01/15/2023] Open
Abstract
PIM1 is an oncogenic kinase overexpressed in a number of cancers where it correlates with poor prognosis. Several studies demonstrated that inhibition of PIM1 activity is an attractive strategy in fighting overexpressing cancers, while distinct structural features of ATP binding pocket make PIM1 an inviting target for the design of selective inhibitors. To facilitate development of specific PIM1 inhibitors, in this study we report three crystal structures of ATP-competitive inhibitors at the ATP binding pocket of PIM1. Two of the reported structures (CX-4945 and Ro-3306) explain the off-target effect on PIM1 of respectively casein kinase 2 and cyclin-dependent kinase 1 dedicated inhibitors. In turn, the structure with CX-6258 demonstrates a binding mode of a potent, selective inhibitor of PIM1, PIM2, PIM3 and Flt-3 kinases. The consequences of our findings for future inhibitor development are discussed.
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12
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Mori M, Tintori C, Christopher RSA, Radi M, Schenone S, Musumeci F, Brullo C, Sanità P, Delle Monache S, Angelucci A, Kissova M, Crespan E, Maga G, Botta M. A combination strategy to inhibit Pim-1: synergism between noncompetitive and ATP-competitive inhibitors. ChemMedChem 2013; 8:484-96. [PMID: 23436791 DOI: 10.1002/cmdc.201200480] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Indexed: 12/30/2022]
Abstract
Pim-1 is a serine/threonine kinase critically involved in the initiation and progression of various types of cancer, especially leukemia, lymphomas and solid tumors such as prostate, pancreas and colon, and is considered a potential drug target against these malignancies. In an effort to discover new potent Pim-1 inhibitors, a previously identified ATP-competitive indolyl-pyrrolone scaffold was expanded to derive structure-activity relationship data. A virtual screening campaign was also performed, which led to the discovery of additional ATP-competitive inhibitors as well as a series of 2-aminothiazole derivatives, which are noncompetitive with respect to both ATP and peptide substrate. This mechanism of action, which resembles allosteric inhibition, has not previously been characterized for Pim-1. Notably, further evaluation of the 2-aminothiazoles indicated a synergistic inhibitory effect in enzymatic assays when tested in combination with ATP-competitive inhibitors. A synergistic effect in the inhibition of cell proliferation by ATP-competitive and ATP-noncompetitive compounds was also observed in prostate cancer cell lines (PC3), where all Pim-1 inhibitors tested in showed synergism with the known anticancer agent, paclitaxel. These results further establish Pim-1 as a target in cancer therapy, and highlight the potential of these agents for use as adjuvant agents in the treatment of cancer diseases in which Pim-1 is associated with chemotherapeutic resistance.
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Affiliation(s)
- Mattia Mori
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
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13
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Lori C, Lantella A, Pasquo A, Alexander LT, Knapp S, Chiaraluce R, Consalvi V. Effect of single amino acid substitution observed in cancer on Pim-1 kinase thermodynamic stability and structure. PLoS One 2013; 8:e64824. [PMID: 23755147 PMCID: PMC3673989 DOI: 10.1371/journal.pone.0064824] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/18/2013] [Indexed: 11/19/2022] Open
Abstract
Pim-1 kinase, a serine/threonine protein kinase encoded by the pim proto-oncogene, is involved in several signalling pathways such as the regulation of cell cycle progression and apoptosis. Many cancer types show high expression levels of Pim kinases and particularly Pim-1 has been linked to the initiation and progression of the malignant phenotype. In several cancer tissues somatic Pim-1 mutants have been identified. These natural variants are nonsynonymous single nucleotide polymorphisms, variations of a single nucleotide occurring in the coding region and leading to amino acid substitutions. In this study we investigated the effect of amino acid substitution on the structural stability and on the activity of Pim-1 kinase. We expressed and purified some of the mutants of Pim-1 kinase that are expressed in cancer tissues and reported in the single nucleotide polymorphisms database. The point mutations in the variants significantly affect the conformation of the native state of Pim-1. All the mutants, expressed as soluble recombinant proteins, show a decreased thermal and thermodynamic stability and a lower activation energy values for kinase activity. The decreased stability accompanied by an increased flexibility suggests that Pim-1 variants may be involved in a wider network of protein interactions. All mutants bound ATP and ATP mimetic inhibitors with comparable IC50 values suggesting that the studied Pim-1 kinase mutants can be efficiently targeted with inhibitors developed for the wild type protein.
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Affiliation(s)
- Clorinda Lori
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Rome, Italy
| | - Antonella Lantella
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Rome, Italy
| | | | - Leila T. Alexander
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Roberta Chiaraluce
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Rome, Italy
- * E-mail:
| | - Valerio Consalvi
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Rome, Italy
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14
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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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15
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Abstract
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Thermal fluctuations cause proteins to adopt an ensemble of conformations wherein the relative stability of the different ensemble members is determined by the topography of the underlying energy landscape. “Folded” proteins have relatively homogeneous ensembles, while “unfolded” proteins have heterogeneous ensembles. Hence, the labels “folded” and “unfolded” represent attempts to provide a qualitative characterization of the extent of structural heterogeneity within the underlying ensemble. In this work, we introduce an information-theoretic order parameter to quantify this conformational heterogeneity. We demonstrate that this order parameter can be estimated in a straightforward manner from an ensemble and is applicable to both unfolded and folded proteins. In addition, a simple formula for approximating the order parameter directly from crystallographic B factors is presented. By applying these metrics to a large sample of proteins, we show that proteins span the full range of the order–disorder axis.
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Affiliation(s)
- Charles K Fisher
- Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, Massachusetts 02139-4307, USA
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16
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Fedorov O, Huber K, Eisenreich A, Filippakopoulos P, King O, Bullock AN, Szklarczyk D, Jensen LJ, Fabbro D, Trappe J, Rauch U, Bracher F, Knapp S. Specific CLK inhibitors from a novel chemotype for regulation of alternative splicing. CHEMISTRY & BIOLOGY 2011; 18:67-76. [PMID: 21276940 PMCID: PMC3145970 DOI: 10.1016/j.chembiol.2010.11.009] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 11/08/2010] [Accepted: 11/10/2010] [Indexed: 12/02/2022]
Abstract
There is a growing recognition of the importance of protein kinases in the control of alternative splicing. To define the underlying regulatory mechanisms, highly selective inhibitors are needed. Here, we report the discovery and characterization of the dichloroindolyl enaminonitrile KH-CB19, a potent and highly specific inhibitor of the CDC2-like kinase isoforms 1 and 4 (CLK1/CLK4). Cocrystal structures of KH-CB19 with CLK1 and CLK3 revealed a non-ATP mimetic binding mode, conformational changes in helix αC and the phosphate binding loop and halogen bonding to the kinase hinge region. KH-CB19 effectively suppressed phosphorylation of SR (serine/arginine) proteins in cells, consistent with its expected mechanism of action. Chemical inhibition of CLK1/CLK4 generated a unique pattern of splicing factor dephosphorylation and had at low nM concentration a profound effect on splicing of the two tissue factor isoforms flTF (full-length TF) and asHTF (alternatively spliced human TF).
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Affiliation(s)
- Oleg Fedorov
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Kilian Huber
- Ludwig-Maximilians Universität, Department of Pharmacy-Center for Drug Research, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Andreas Eisenreich
- Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Centrum für Herz-und Kreislaufmedizin, Berlin, Germany
| | - Panagis Filippakopoulos
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Oliver King
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Alex N. Bullock
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Damian Szklarczyk
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Denmark
| | - Lars J. Jensen
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Denmark
| | - Doriano Fabbro
- Novartis Pharma AG, Klybeckstrasse 141, CH-4002 Basel, Switzerland
| | - Jörg Trappe
- Novartis Pharma AG, Klybeckstrasse 141, CH-4002 Basel, Switzerland
| | - Ursula Rauch
- Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Centrum für Herz-und Kreislaufmedizin, Berlin, Germany
| | - Franz Bracher
- Ludwig-Maximilians Universität, Department of Pharmacy-Center for Drug Research, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Stefan Knapp
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Old Road Campus Research Building, Oxford OX3 7DQ, UK
- University of Oxford, Department of Clinical Pharmacology, Old Road Campus Research Building, Oxford OX3 7DQ, UK
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