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Abdelaziz ME, El-Miligy MMM, Fahmy SM, Abu-Serie MM, Hazzaa AA, Mahran MA. Imparting aromaticity to 2-pyridone derivatives by O-alkylation resulted in new competitive and non-competitive PIM-1 kinase inhibitors with caspase-activated apoptosis. J Enzyme Inhib Med Chem 2024; 39:2304044. [PMID: 38230430 PMCID: PMC10795791 DOI: 10.1080/14756366.2024.2304044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/07/2024] [Indexed: 01/18/2024] Open
Abstract
New aromatic O-alkyl pyridine derivatives were designed and synthesised as Proviral Integration Moloney (PIM)-1 kinase inhibitors. 4c and 4f showed potent in vitro anticancer activity against NFS-60, HepG-2, PC-3, and Caco-2 cell lines and low toxicity against normal human lung fibroblast Wi-38 cell line. Moreover, 4c and 4f induced apoptosis in the four tested cancer cell lines with high percentage. In addition, 4c and 4f significantly induced caspase 3/7 activation in HepG-2 cell line. Furthermore, 4c and 4f showed potent PIM-1 kinase inhibitory activity with IC50 = 0.110, 0.095 µM, respectively. Kinetic studies indicated that 4c and 4f were both competitive and non-competitive inhibitors for PIM-1 kinase enzyme. In addition, in silico prediction of physiochemical properties, pharmacokinetic profile, ligand efficiency, ligand lipophilic efficiency, and induced fit docking studies were consistent with the biological and kinetic studies, and predicted that 4c and 4f could act as PIM-1 kinase competitive non-adenosine triphosphate (ATP) mimetics with drug like properties.
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Affiliation(s)
- Marwa E. Abdelaziz
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Mostafa M. M. El-Miligy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Salwa M. Fahmy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Marwa M. Abu-Serie
- Medical Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), Alexandria, Egypt
| | - Aly A. Hazzaa
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Mona A. Mahran
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
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2
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Hochban PMM, Heyder L, Heine A, Diederich WE. What doesn't fit is made to fit: Pim-1 kinase adapts to the configuration of stilbene-based inhibitors. Arch Pharm (Weinheim) 2024; 357:e2400094. [PMID: 38631036 DOI: 10.1002/ardp.202400094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/19/2024]
Abstract
Recently, we have developed novel Pim-1 kinase inhibitors starting from a dihydrobenzofuran core structure using a computational approach. Here, we report the design and synthesis of stilbene-based Pim-1 kinase inhibitors obtained by formal elimination of the dihydrofuran ring. These inhibitors of the first design cycle, which were obtained as inseparable cis/trans mixtures, showed affinities in the low single-digit micromolar range. To be able to further optimize these compounds in a structure-based fashion, we determined the X-ray structures of the protein-ligand-complexes. Surprisingly, only the cis-isomer binds upon crystallization of the cis/trans-mixture of the ligands with Pim-1 kinase and the substrate PIMTIDE, the binding mode being largely consistent with that predicted by docking. After crystallization of the exclusively trans-configured derivatives, a markedly different binding mode for the inhibitor and a concomitant rearrangement of the glycine-rich loop is observed, resulting in the ligand being deeply buried in the binding pocket.
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Affiliation(s)
- Phil M M Hochban
- Institut für Pharmazeutische Chemie, Zentrum für Tumor und Immunbiologie, Philipps-Universität Marburg, Marburg, Germany
| | - Lukas Heyder
- Institut für Pharmazeutische Chemie, Zentrum für Tumor und Immunbiologie, Philipps-Universität Marburg, Marburg, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Wibke E Diederich
- Institut für Pharmazeutische Chemie, Zentrum für Tumor und Immunbiologie, Philipps-Universität Marburg, Marburg, Germany
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3
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Tantawy ES, Nafie MS, Morsy HA, El-Sayed HA, Moustafa AH, Mohammed SM. Synthesis of novel bioactive pyrido[2,3- d]pyrimidine derivatives with potent cytotoxicity through apoptosis as PIM-1 kinase inhibitors. RSC Adv 2024; 14:11098-11111. [PMID: 38586446 PMCID: PMC10996840 DOI: 10.1039/d4ra00902a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 03/30/2024] [Indexed: 04/09/2024] Open
Abstract
Direct synthesis and cytotoxicity activity of new series of pyrido[2,3-d]pyrimidine was described. Nicotinamide 2 was synthesized via cyclization of N-cyclohexyl derivative with cyanoacetamide. The o-aminonicotinonitrile 2 was subjected to acylation or thio acylation process followed by intramolecular heterocyclization to afford the desired pyrido[2,3-d]pyrimidine (3-10) and pyrido triazine 11. Compounds 4 and 11 exhibited remarkable cytotoxicity against MCF-7 cells with IC50 values of 0.57 μM and 1.31 μM and IC50 values of 1.13 μM and 0.99 μM against HepG2 cells. Interestingly, compounds 4 and 10 had potent PIM-1 kinase inhibition with IC50 values of 11.4 and 17.2 nM, respectively, with inhibition of 97.8% and 94.6% compared to staurosporine (IC50 = 16.7 nM, with 95.6% inhibition). Moreover, compound 4 significantly activated apoptosis in MCF-7 cells, increasing the cell apoptosis by 58.29-fold by having 36.14% total apoptosis in treated cells compared to 0.62% for control. Moreover, it arrested the cell cycle at the G1 phase. PIM-1 kinase inhibition was virtually elucidated by the molecular docking study, highlighting binding interactions of the lead compound 4 towards the PIM-1 protein. Accordingly, compound 4 was validated as a promising PIM-1 targeted chemotherapeutic agent to treat breast cancer.
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Affiliation(s)
- Eman S Tantawy
- Department of Chemistry, Faculty of Science, Zagazig University Zagazig 44519 Egypt
| | - Mohamed S Nafie
- Department of Chemistry, College of Sciences, University of Sharjah P. O. 27272 Sharjah United Arab Emirates
- Chemistry Department, Faculty of Science, Suez Canal University P. O. 41522 Ismailia Egypt
| | - Hesham A Morsy
- Higher Institution of Engineering & Modern Technology Elmarg Cairo 13774 Egypt
| | - Hassan A El-Sayed
- Department of Chemistry, Faculty of Science, Zagazig University Zagazig 44519 Egypt
| | - Ahmed H Moustafa
- Department of Chemistry, Faculty of Science, Zagazig University Zagazig 44519 Egypt
| | - Samar M Mohammed
- Department of Chemistry, Faculty of Science, Zagazig University Zagazig 44519 Egypt
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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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Park H, Jeon J, Kim K, Choi S, Hong S. Structure-Based Virtual Screening and De Novo Design of PIM1 Inhibitors with Anticancer Activity from Natural Products. Pharmaceuticals (Basel) 2021; 14:ph14030275. [PMID: 33803840 PMCID: PMC8003278 DOI: 10.3390/ph14030275] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND the proviral insertion site of Moloney murine leukemia (PIM) 1 kinase has served as a therapeutic target for various human cancers due to the enhancement of cell proliferation and the inhibition of apoptosis. METHODS to identify effective PIM1 kinase inhibitors, structure-based virtual screening of natural products of plant origin and de novo design were carried out using the protein-ligand binding free energy function improved by introducing an adequate dehydration energy term. RESULTS as a consequence of subsequent enzyme inhibition assays, four classes of PIM1 kinase inhibitors were discovered, with the biochemical potency ranging from low-micromolar to sub-micromolar levels. The results of extensive docking simulations showed that the inhibitory activity stemmed from the formation of multiple hydrogen bonds in combination with hydrophobic interactions in the ATP-binding site. Optimization of the biochemical potency by chemical modifications of the 2-benzylidenebenzofuran-3(2H)-one scaffold led to the discovery of several nanomolar inhibitors with antiproliferative activities against human breast cancer cell lines. CONCLUSIONS these new PIM1 kinase inhibitors are anticipated to serve as a new starting point for the development of anticancer medicine.
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Affiliation(s)
- Hwangseo Park
- Department of Bioscience and Biotechnology and Institute of Anticancer Medicine Development, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul 05006, Korea
- Correspondence: (H.P.); (S.H.); Tel.: +82-23-408-3766 (H.P.); +82-42-350-2811 (S.H.)
| | - Jinwon Jeon
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea; (J.J.); (K.K.); (S.C.)
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Kewon Kim
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea; (J.J.); (K.K.); (S.C.)
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Soyeon Choi
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea; (J.J.); (K.K.); (S.C.)
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Sungwoo Hong
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea; (J.J.); (K.K.); (S.C.)
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Correspondence: (H.P.); (S.H.); Tel.: +82-23-408-3766 (H.P.); +82-42-350-2811 (S.H.)
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Creixell P, Pandey JP, Palmeri A, Bhattacharyya M, Creixell M, Ranganathan R, Pincus D, Yaffe MB. Hierarchical Organization Endows the Kinase Domain with Regulatory Plasticity. Cell Syst 2018; 7:371-383.e4. [PMID: 30243563 DOI: 10.1016/j.cels.2018.08.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/24/2018] [Accepted: 08/13/2018] [Indexed: 02/08/2023]
Abstract
The functional diversity of kinases enables specificity in cellular signal transduction. Yet how more than 500 members of the human kinome specifically receive regulatory inputs and convey information to appropriate substrates-all while using the common signaling output of phosphorylation-remains enigmatic. Here, we perform statistical co-evolution analysis, mutational scanning, and quantitative live-cell assays to reveal a hierarchical organization of the kinase domain that facilitates the orthogonal evolution of regulatory inputs and substrate outputs while maintaining catalytic function. We find that three quasi-independent "sectors"-groups of evolutionarily coupled residues-represent functional units in the kinase domain that encode for catalytic activity, substrate specificity, and regulation. Sector positions impact both disease and pharmacology: the catalytic sector is significantly enriched for somatic cancer mutations, and residues in the regulatory sector interact with allosteric kinase inhibitors. We propose that this functional architecture endows the kinase domain with inherent regulatory plasticity.
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Affiliation(s)
- Pau Creixell
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jai P Pandey
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Moitrayee Bhattacharyya
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Marc Creixell
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rama Ranganathan
- Center for Physics of Evolving Systems, Department of Biochemistry and Molecular Biology, Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - David Pincus
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
| | - Michael B Yaffe
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Surgery, Beth Israel Deaconess Medical Center, Divisions of Acute Care Surgery, Trauma, and Critical Care and Surgical Oncology, Harvard Medical School, Boston 02215, USA.
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Lee SJ, Han BG, Cho JW, Choi JS, Lee J, Song HJ, Koh JS, Lee BI. Correction: Crystal Structure of Pim1 Kinase in Complex with a Pyrido[4,3-D]Pyrimidine Derivative Suggests a Unique Binding Mode. PLoS One 2018; 13:e0190843. [PMID: 29293667 PMCID: PMC5749892 DOI: 10.1371/journal.pone.0190843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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8
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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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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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