1
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Sobierajski T, Małolepsza J, Pichlakb M, Gendaszewska-Darmach E, Błażewska KM. The impact of E3 ligase choice on PROTAC effectiveness in protein kinase degradation. Drug Discov Today 2024:104032. [PMID: 38789027 DOI: 10.1016/j.drudis.2024.104032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/30/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024]
Abstract
Proteolysis targeting chimera (PROTACs) provide a novel therapeutic approach that is revolutionizing drug discovery. The success of PROTACs largely depends on the combination of their three fragments: E3 ligase ligand, linker and protein of interest (POI)-targeting ligand. We summarize the pivotal significance of the precise combination of the E3 ligase ligand with the POI-recruiting warhead, which is crucial for the successful execution of cellular processes and achieving the desired outcomes. Therefore, the key to selection was the use of at least two ligands recruiting two different ligases. This approach enables a direct comparison of the impacts of the specific ligases on target degradation.
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Affiliation(s)
- Tomasz Sobierajski
- Institute of Organic Chemistry, Lodz University of Technology, Łódź, Poland
| | - Joanna Małolepsza
- Institute of Organic Chemistry, Lodz University of Technology, Łódź, Poland
| | - Marta Pichlakb
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Łódź, Poland
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2
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Rak M, Menge A, Tesch R, Berger LM, Balourdas DI, Shevchenko E, Krämer A, Elson L, Berger BT, Abdi I, Wahl LM, Poso A, Kaiser A, Hanke T, Kronenberger T, Joerger AC, Müller S, Knapp S. Development of Selective Pyrido[2,3- d]pyrimidin-7(8 H)-one-Based Mammalian STE20-Like (MST3/4) Kinase Inhibitors. J Med Chem 2024; 67:3813-3842. [PMID: 38422480 DOI: 10.1021/acs.jmedchem.3c02217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Mammalian STE20-like (MST) kinases 1-4 play key roles in regulating the Hippo and autophagy pathways, and their dysregulation has been implicated in cancer development. In contrast to the well-studied MST1/2, the roles of MST3/4 are less clear, in part due to the lack of potent and selective inhibitors. Here, we re-evaluated literature compounds, and used structure-guided design to optimize the p21-activated kinase (PAK) inhibitor G-5555 (8) to selectively target MST3/4. These efforts resulted in the development of MR24 (24) and MR30 (27) with good kinome-wide selectivity and high cellular potency. The distinct cellular functions of closely related MST kinases can now be elucidated with subfamily-selective chemical tool compounds using a combination of the MST1/2 inhibitor PF-06447475 (2) and the two MST3/4 inhibitors developed. We found that MST3/4-selective inhibition caused a cell-cycle arrest in the G1 phase, whereas MST1/2 inhibition resulted in accumulation of cells in the G2/M phase.
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Affiliation(s)
- Marcel Rak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Amelie Menge
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Roberta Tesch
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Lena M Berger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Dimitrios-Ilias Balourdas
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Ekaterina Shevchenko
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
- German Translational Cancer Network (DKTK) and Frankfurt Cancer Institute (FCI), 60438 Frankfurt am Main, Germany
| | - Lewis Elson
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Benedict-Tilman Berger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Ismahan Abdi
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Laurenz M Wahl
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, 70210 Kuopio, Finland
| | - Astrid Kaiser
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Thomas Hanke
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, 70210 Kuopio, Finland
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
- German Translational Cancer Network (DKTK) and Frankfurt Cancer Institute (FCI), 60438 Frankfurt am Main, Germany
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3
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Champion C, Gall R, Ries B, Rieder SR, Barros EP, Riniker S. Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases. J Chem Inf Model 2023; 63:7133-7147. [PMID: 37948537 PMCID: PMC10685456 DOI: 10.1021/acs.jcim.3c01469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Abstract
Alchemical free-energy methods based on molecular dynamics (MD) simulations have become important tools to identify modifications of small organic molecules that improve their protein binding affinity during lead optimization. The routine application of pairwise free-energy methods to rank potential binders from best to worst is impacted by the combinatorial increase in calculations to perform when the number of molecules to assess grows. To address this fundamental limitation, our group has developed replica-exchange enveloping distribution sampling (RE-EDS), a pathway-independent multistate method, enabling the calculation of alchemical free-energy differences between multiple ligands (N > 2) from a single MD simulation. In this work, we apply the method to a set of four kinases with diverse binding pockets and their corresponding inhibitors (42 in total), chosen to showcase the general applicability of RE-EDS in prospective drug design campaigns. We show that for the targets studied, RE-EDS is able to model up to 13 ligands simultaneously with high sampling efficiency, leading to a substantial decrease in computational cost when compared to pairwise methods.
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Affiliation(s)
- Candide Champion
- Department of Chemistry and
Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - René Gall
- Department of Chemistry and
Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | | | - Salomé R. Rieder
- Department of Chemistry and
Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Emilia P. Barros
- Department of Chemistry and
Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Sereina Riniker
- Department of Chemistry and
Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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4
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Belli S, Pesapane A, Servetto A, Esposito D, Napolitano F, Ascione CM, Allotta A, Zambrano N, Marino FZ, Franco R, Troiani T, Formisano L, Bianco R. Combined blockade of mTOR and p21-activated kinases pathways prevents tumour growth in KRAS-mutated colorectal cancer. Br J Cancer 2023; 129:1071-1082. [PMID: 37568037 PMCID: PMC10539494 DOI: 10.1038/s41416-023-02390-z] [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: 10/29/2022] [Revised: 07/04/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND The identification of novel therapeutic strategies for metastatic colorectal cancer (mCRC) patients harbouring KRAS mutations represents an unmet clinical need. In this study, we aimed to clarify the role of p21-activated kinases (Paks) as therapeutic target for KRAS-mutated CRC. METHODS Paks expression and activation levels were evaluated in a cohort of KRAS-WT or -mutated CRC patients by immunohistochemistry. The effects of Paks inhibition on tumour cell proliferation and signal transduction were assayed by RNAi and by the use of three pan-Paks inhibitors (PF-3758309, FRAX1036, GNE-2861), evaluating CRC cells, spheroids and tumour xenografts' growth. RESULTS Paks activation positively correlated with KRAS mutational status in both patients and cell lines. Moreover, genetic modulation or pharmacological inhibition of Paks led to a robust impairment of KRAS-mut CRC cell proliferation. However, Paks prolonged blockade induced a rapid tumour adaptation through the hyper-activation of the mTOR/p70S6K pathway. The addition of everolimus (mTOR inhibitor) prevented the growth of KRAS-mut CRC tumours in vitro and in vivo, reverting the adaptive tumour resistance to Paks targeting. CONCLUSIONS In conclusion, our results suggest the simultaneous blockade of mTOR and Pak pathways as a promising alternative therapeutic strategy for patients affected by KRAS-mut colorectal cancer.
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Affiliation(s)
- Stefania Belli
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131, Naples, Italy
| | - Ada Pesapane
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131, Naples, Italy
| | - Alberto Servetto
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131, Naples, Italy
| | - Daniela Esposito
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131, Naples, Italy
| | - Fabiana Napolitano
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131, Naples, Italy
| | - Claudia Maria Ascione
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131, Naples, Italy
| | - Alessandra Allotta
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131, Naples, Italy
| | - Nicola Zambrano
- CEINGE Biotecnologie Avanzate S.C.aR.L., Via G. Salvatore 486, 80145, Naples, Italy
| | | | - Renato Franco
- Pathology Unit, University of Campania "L. Vanvitelli", Naples, Italy
| | - Teresa Troiani
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Naples, Italy
| | - Luigi Formisano
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131, Naples, Italy.
| | - Roberto Bianco
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131, Naples, Italy.
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5
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Rak M, Tesch R, Berger LM, Shevchenko E, Raab M, Tjaden A, Zhubi R, Balourdas DI, Joerger AC, Poso A, Krämer A, Elson L, Lučić A, Kronenberger T, Hanke T, Strebhardt K, Sanhaji M, Knapp S. Shifting the selectivity of pyrido[2,3-d]pyrimidin-7(8H)-one inhibitors towards the salt-inducible kinase (SIK) subfamily. Eur J Med Chem 2023; 254:115347. [PMID: 37094449 DOI: 10.1016/j.ejmech.2023.115347] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/27/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023]
Abstract
Salt-inducible kinases 1-3 (SIK1-3) are key regulators of the LKB1-AMPK pathway and play an important role in cellular homeostasis. Dysregulation of any of the three isoforms has been associated with tumorigenesis in liver, breast, and ovarian cancers. We have recently developed the dual pan-SIK/group I p21-activated kinase (PAK) chemical probe MRIA9. However, inhibition of p21-activated kinases has been associated with cardiotoxicity in vivo, which complicates the use of MRIA9 as a tool compound. Here, we present a structure-based approach involving the back-pocket and gatekeeper residues, for narrowing the selectivity of pyrido[2,3-d]pyrimidin-7(8H)-one-based inhibitors towards SIK kinases, eliminating PAK activity. Optimization was guided by high-resolution crystal structure analysis and computational methods, resulting in a pan-SIK inhibitor, MR22, which no longer exhibited activity on STE group kinases and displayed excellent selectivity in a representative kinase panel. MR22-dependent SIK inhibition led to centrosome dissociation and subsequent cell-cycle arrest in ovarian cancer cells, as observed with MRIA9, conclusively linking these phenotypic effects to SIK inhibition. Taken together, MR22 represents a valuable tool compound for studying SIK kinase function in cells.
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Affiliation(s)
- Marcel Rak
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Roberta Tesch
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Lena M Berger
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Ekaterina Shevchenko
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen, 72076, Germany; School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, Kuopio, 70210, Finland
| | - Monika Raab
- Department of Obstetrics and Gynaecology, School of Medicine, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany
| | - Amelie Tjaden
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Rezart Zhubi
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Dimitrios-Ilias Balourdas
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen, 72076, Germany; School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, Kuopio, 70210, Finland
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany; German Translational Cancer Network (DKTK) and Frankfurt Cancer Institute (FCI), Frankfurt am Main, 60438, Germany
| | - Lewis Elson
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Aleksandar Lučić
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen, 72076, Germany; School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, Kuopio, 70210, Finland
| | - Thomas Hanke
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Klaus Strebhardt
- Department of Obstetrics and Gynaecology, School of Medicine, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany
| | - Mourad Sanhaji
- Department of Obstetrics and Gynaecology, School of Medicine, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany; German Translational Cancer Network (DKTK) and Frankfurt Cancer Institute (FCI), Frankfurt am Main, 60438, Germany.
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6
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Brindani N, Vuong LM, Acquistapace IM, La Serra MA, Ortega JA, Veronesi M, Bertozzi SM, Summa M, Girotto S, Bertorelli R, Armirotti A, Ganesan AK, De Vivo M. Design, Synthesis, In Vitro and In Vivo Characterization of CDC42 GTPase Interaction Inhibitors for the Treatment of Cancer. J Med Chem 2023; 66:5981-6001. [PMID: 37026468 PMCID: PMC10150367 DOI: 10.1021/acs.jmedchem.3c00276] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Indexed: 04/08/2023]
Abstract
CDC42 GTPases (RHOJ, CDC42, and RHOQ) are overexpressed in multiple tumor types and activate pathways critical for tumor growth, angiogenesis, and metastasis. Recently, we reported the discovery of a novel lead compound, ARN22089, which blocks the interaction of CDC42 GTPases with specific downstream effectors. ARN22089 blocks tumor growth in BRAF mutant mouse melanoma models and patient-derived xenografts (PDXs) in vivo. ARN22089 also inhibits tumor angiogenesis in three-dimensional vascularized microtumor models in vitro. Notably, ARN22089 belongs to a novel class of trisubstituted pyrimidines. Based on these results, we describe an extensive structure-activity relationship of ∼30 compounds centered on ARN22089. We discovered and optimized two novel inhibitors (27, ARN25062, and 28, ARN24928), which are optimal back-up/follow-up leads with favorable drug-like properties and in vivo efficacy in PDX tumors. These findings further demonstrate the potential of this class of CDC42/RHOJ inhibitors for cancer treatment, with lead candidates ready for advanced preclinical studies.
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Affiliation(s)
- Nicoletta Brindani
- Molecular
Modeling and Drug Discovery Lab, Istituto
Italiano di Tecnologia, Via Morego 30, Genova 16163, Italy
| | - Linh M. Vuong
- Department
of Dermatology, University of California, Irvine, California 92697, United States
| | - Isabella Maria Acquistapace
- Molecular
Modeling and Drug Discovery Lab, Istituto
Italiano di Tecnologia, Via Morego 30, Genova 16163, Italy
| | - Maria Antonietta La Serra
- Molecular
Modeling and Drug Discovery Lab, Istituto
Italiano di Tecnologia, Via Morego 30, Genova 16163, Italy
| | - José Antonio Ortega
- Molecular
Modeling and Drug Discovery Lab, Istituto
Italiano di Tecnologia, Via Morego 30, Genova 16163, Italy
| | - Marina Veronesi
- Structural
Biophysics Facility, Istituto Italiano di
Tecnologia, Via Morego
30, Genova 16163, Italy
| | - Sine Mandrup Bertozzi
- Analytical
Chemistry Facility, Istituto Italiano di
Tecnologia, Via Morego
30, Genova 16163, Italy
| | - Maria Summa
- Translational
Pharmacology Facility, Istituto Italiano
di Tecnologia, Via Morego
30, Genova 16163, Italy
| | - Stefania Girotto
- Structural
Biophysics Facility, Istituto Italiano di
Tecnologia, Via Morego
30, Genova 16163, Italy
| | - Rosalia Bertorelli
- Translational
Pharmacology Facility, Istituto Italiano
di Tecnologia, Via Morego
30, Genova 16163, Italy
| | - Andrea Armirotti
- Analytical
Chemistry Facility, Istituto Italiano di
Tecnologia, Via Morego
30, Genova 16163, Italy
| | - Anand K. Ganesan
- Department
of Dermatology, University of California, Irvine, California 92697, United States
| | - Marco De Vivo
- Molecular
Modeling and Drug Discovery Lab, Istituto
Italiano di Tecnologia, Via Morego 30, Genova 16163, Italy
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7
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Somanath PR, Chernoff J, Cummings BS, Prasad SM, Homan HD. Targeting P21-Activated Kinase-1 for Metastatic Prostate Cancer. Cancers (Basel) 2023; 15:cancers15082236. [PMID: 37190165 DOI: 10.3390/cancers15082236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/06/2023] [Accepted: 04/09/2023] [Indexed: 05/17/2023] Open
Abstract
Metastatic prostate cancer (mPCa) has limited therapeutic options and a high mortality rate. The p21-activated kinase (PAK) family of proteins is important in cell survival, proliferation, and motility in physiology, and pathologies such as infectious, inflammatory, vascular, and neurological diseases as well as cancers. Group-I PAKs (PAK1, PAK2, and PAK3) are involved in the regulation of actin dynamics and thus are integral for cell morphology, adhesion to the extracellular matrix, and cell motility. They also play prominent roles in cell survival and proliferation. These properties make group-I PAKs a potentially important target for cancer therapy. In contrast to normal prostate and prostatic epithelial cells, group-I PAKs are highly expressed in mPCA and PCa tissue. Importantly, the expression of group-I PAKs is proportional to the Gleason score of the patients. While several compounds have been identified that target group-I PAKs and these are active in cells and mice, and while some inhibitors have entered human trials, as of yet, none have been FDA-approved. Probable reasons for this lack of translation include issues related to selectivity, specificity, stability, and efficacy resulting in side effects and/or lack of efficacy. In the current review, we describe the pathophysiology and current treatment guidelines of PCa, present group-I PAKs as a potential druggable target to treat mPCa patients, and discuss the various ATP-competitive and allosteric inhibitors of PAKs. We also discuss the development and testing of a nanotechnology-based therapeutic formulation of group-I PAK inhibitors and its significant potential advantages as a novel, selective, stable, and efficacious mPCa therapeutic over other PCa therapeutics in the pipeline.
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Affiliation(s)
- Payaningal R Somanath
- Department of Clinical & Administrative Pharmacy, College of Pharmacy, University of Georgia, Augusta, GA 30912, USA
- MetasTx LLC, Basking Ridge, NJ 07920, USA
| | - Jonathan Chernoff
- MetasTx LLC, Basking Ridge, NJ 07920, USA
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Brian S Cummings
- MetasTx LLC, Basking Ridge, NJ 07920, USA
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Sandip M Prasad
- Morristown Medical Center, Atlantic Health System, Morristown, NJ 07960, USA
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8
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Chow HY, Karchugina S, Groendyke BJ, Toenjes S, Hatcher J, Donovan KA, Fischer ES, Abalakov G, Faezov B, Dunbrack R, Gray NS, Chernoff J. Development and Utility of a PAK1-Selective Degrader. J Med Chem 2022; 65:15627-15641. [PMID: 36416208 PMCID: PMC10029980 DOI: 10.1021/acs.jmedchem.2c00756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Overexpression of PAK1, a druggable kinase, is common in several malignancies, and inhibition of PAK1 by small molecules has been shown to impede the growth and survival of such cells. Potent inhibitors of PAKs 1-3 have been described, but clinical development has been hindered by recent findings that PAK2 function is required for normal cardiovascular function in adult mice. A unique allosteric PAK1-selective inhibitor, NVS-PAK1-1, provides a potential path forward, but has modest potency. Here, we report the development of BJG-05-039, a PAK1-selective degrader consisting of NVS-PAK1-1 conjugated to lenalidomide, a recruiter of the E3 ubiquitin ligase substrate adaptor Cereblon. BJG-05-039 induced selective degradation of PAK1 and displayed enhanced anti-proliferative effects relative to its parent compound in PAK1-dependent, but not PAK2-dependent, cell lines. Our findings suggest that selective PAK1 degradation may confer more potent pharmacological effects compared with catalytic inhibition and highlight the potential advantages of PAK1-targeted degradation.
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Affiliation(s)
- Hoi-Yee Chow
- Fox Chase Cancer Center, Philadelphia, PA 19111
- National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, China 610041
| | | | - Brian J. Groendyke
- Department of Cancer Biology; Dana Farber Cancer Institute, Boston, MA 02215
- Current address: Blueprint Medicines, Cambridge, MA 02139
| | - Sean Toenjes
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA 94305
| | - John Hatcher
- Department of Cancer Biology; Dana Farber Cancer Institute, Boston, MA 02215
| | - Katherine A. Donovan
- Department of Cancer Biology; Dana Farber Cancer Institute, Boston, MA 02215
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215
| | - Eric S. Fischer
- Department of Cancer Biology; Dana Farber Cancer Institute, Boston, MA 02215
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215
| | | | - Bulat Faezov
- Fox Chase Cancer Center, Philadelphia, PA 19111
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation, 420008
| | | | - Nathanael S. Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA 94305
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9
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Komkov AV, Sukhanova AА, Menchikov LG, Zavarzin IV. о-Aminopyrimidine Aldehydes and Ketones: Synthesis and use as Precursors to Fused Pyrimidines. Chem Heterocycl Compd (N Y) 2022. [DOI: 10.1007/s10593-022-03141-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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10
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Li Y, Lu Q, Xie C, Yu Y, Zhang A. Recent advances on development of p21-activated kinase 4 inhibitors as anti-tumor agents. Front Pharmacol 2022; 13:956220. [PMID: 36105226 PMCID: PMC9465411 DOI: 10.3389/fphar.2022.956220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/20/2022] [Indexed: 12/05/2022] Open
Abstract
The p21-activated kinase 4 (PAK4) is a member of the PAKs family. It is overexpressed in multiple tumor tissues. Pharmacological inhibition of PAK4 attenuates proliferation, migration, and invasion of cancer cells. Recent studies revealed that inhibition of PAK4 sensitizes immunotherapy which has been extensively exploited as a new strategy to treat cancer. In the past few years, a large number of PAK4 inhibitors have been reported. Of note, the allosteric inhibitor KPT-9274 has been tested in phase Ⅰ clinic trials. Herein, we provide an update on recent research progress on the PAK4 mediated signaling pathway and highlight the development of the PAK4 small molecular inhibitors in recent 5 years. Meanwhile, challenges, limitations, and future developmental directions will be discussed as well.
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Affiliation(s)
- Yang Li
- Pharm-X Center, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Lu
- Pharm-X Center, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Chenghu Xie
- Pharm-X Center, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yiming Yu
- Pharm-X Center, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ao Zhang
- Pharm-X Center, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Ao Zhang,
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11
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P21-activated kinase 2-mediated β-catenin signaling promotes cancer stemness and osimertinib resistance in EGFR-mutant non-small-cell lung cancer. Oncogene 2022; 41:4318-4329. [DOI: 10.1038/s41388-022-02438-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 08/03/2022] [Accepted: 08/08/2022] [Indexed: 11/08/2022]
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12
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Sementino E, Kadariya Y, Cheung M, Menges CW, Tan Y, Kukuyan AM, Shrestha U, Karchugina S, Cai KQ, Peri S, Duncan JS, Chernoff J, Testa JR. Inactivation of p21-Activated Kinase 2 (Pak2) Inhibits the Development of Nf2-Deficient Tumors by Restricting Downstream Hedgehog and Wnt Signaling. Mol Cancer Res 2022; 20:699-711. [PMID: 35082167 PMCID: PMC9081258 DOI: 10.1158/1541-7786.mcr-21-0837] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/02/2021] [Accepted: 01/13/2022] [Indexed: 11/16/2022]
Abstract
Because loss of the NF2 tumor suppressor gene results in p21-activated kinase (Pak) activation, PAK inhibitors hold promise for the treatment of NF2-deficient tumors. To test this possibility, we asked if loss of Pak2, a highly expressed group I PAK member, affects the development of malignant mesothelioma in Nf2;Cdkn2a-deficient (NC) mice and the growth properties of NC mesothelioma cells in culture. In vivo, deletion of Pak2 resulted in a markedly decreased incidence and delayed onset of both pleural and peritoneal malignant mesotheliomas in NC mice. In vitro, Pak2 deletion decreased malignant mesothelioma cell viability, migration, clonogenicity, and spheroid formation. RNA-sequencing analysis demonstrated downregulated expression of Hedgehog and Wnt pathway genes in NC;Pak2-/- mesothelioma cells versus NC;Pak2+/+ mesothelioma cells. Targeting of the Hedgehog signaling component Gli1 or its target gene Myc inhibited cell viability and spheroid formation in NC;P+/+ mesothelioma cells. Kinome profiling uncovered kinase changes indicative of EMT in NC;Pak2-/- mesothelioma cells, suggesting that Pak2-deficient malignant mesotheliomas can adapt by reprogramming their kinome in the absence of Pak activity. The identification of such compensatory pathways offers opportunities for rational combination therapies to circumvent resistance to anti-PAK drugs. IMPLICATIONS We provide evidence supporting a role for PAK inhibitors in treating NF2-deficient tumors. NF2-deficient tumors lacking Pak2 eventually adapt by kinome reprogramming, presenting opportunities for combination therapies to bypass anti-PAK drug resistance.
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Affiliation(s)
- Eleonora Sementino
- Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Yuwaraj Kadariya
- Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Mitchell Cheung
- Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Craig W. Menges
- Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Yinfei Tan
- Genomics Facility, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Anna-Mariya Kukuyan
- Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Ujjawal Shrestha
- Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Sofiia Karchugina
- Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Kathy Q. Cai
- Histopathology Facility, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Suraj Peri
- Bioinformatics and Biostatistics Facility, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - James S. Duncan
- Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Jonathan Chernoff
- Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Joseph R. Testa
- Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Joseph R. Testa, Ph.D., Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 1911; Phone: (215) 728-2610; Fax: (215) 214-1619;
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13
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Wang Y, Guo F. Group I PAKs in myelin formation and repair of the central nervous system: what, when, and how. Biol Rev Camb Philos Soc 2021; 97:615-639. [PMID: 34811887 DOI: 10.1111/brv.12815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 10/20/2021] [Accepted: 11/04/2021] [Indexed: 11/30/2022]
Abstract
p21-activated kinases (PAKs) are a family of cell division control protein 42/ras-related C3 botulinum toxin substrate 1 (Cdc42/Rac1)-activated serine/threonine kinases. Group I PAKs (PAK1-3) have distinct activation mechanisms from group II PAKs (PAK4-6) and are the focus of this review. In transformed cancer cells, PAKs regulate a variety of cellular processes and molecular pathways which are also important for myelin formation and repair in the central nervous system (CNS). De novo mutations in group I PAKs are frequently seen in children with neurodevelopmental defects and white matter anomalies. Group I PAKs regulate virtually every aspect of neuronal development and function. Yet their functions in CNS myelination and remyelination remain incompletely defined. Herein, we highlight the current understanding of PAKs in regulating cellular and molecular pathways and discuss the status of PAK-regulated pathways in oligodendrocyte development. We point out outstanding questions and future directions in the research field of group I PAKs and oligodendrocyte development.
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Affiliation(s)
- Yan Wang
- Department of Neurology, Shriners Hospitals for Children/School of Medicine, Institute for Pediatric Regenerative Medicine (IPRM), University of California, Davis, 2425 Stockton Blvd, Sacramento, CA, 95817, U.S.A
| | - Fuzheng Guo
- Department of Neurology, Shriners Hospitals for Children/School of Medicine, Institute for Pediatric Regenerative Medicine (IPRM), University of California, Davis, 2425 Stockton Blvd, Sacramento, CA, 95817, U.S.A
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14
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p21-Activated kinase 1 (PAK1) in aging and longevity: An overview. Ageing Res Rev 2021; 71:101443. [PMID: 34390849 DOI: 10.1016/j.arr.2021.101443] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 07/26/2021] [Accepted: 08/10/2021] [Indexed: 02/08/2023]
Abstract
The p21-activated kinases (PAKs) belong to serine/threonine kinases family, regulated by ∼21 kDa small signaling G proteins RAC1 and CDC42. The mammalian PAK family comprises six members (PAK1-6) that are classified into two groups (I and II) based on their domain architecture and regulatory mechanisms. PAKs are implicated in a wide range of cellular functions. PAK1 has recently attracted increasing attention owing to its involvement in oncogenesis, tumor progression, and metastasis as well as several life-limiting diseases and pathological conditions. In Caenorhabditis elegans, PAK1 functions limit the lifespan under basal conditions by inhibiting forkhead transcription factor DAF-16. Interestingly, PAK depletion extended longevity and attenuated the onset of age-related phenotypes in a premature-aging mouse model and delayed senescence in mammalian fibroblasts. These observations implicate PAKs as not only oncogenic but also aging kinases. Therefore, PAK-targeting genetic and/or pharmacological interventions, particularly PAK1-targeting, could be a viable strategy for developing cancer therapies with relatively no side effects and promoting healthy longevity. This review describes PAK family proteins, their biological functions, and their role in regulating aging and longevity using C. elegans. Moreover, we discuss the effect of small-molecule PAK1 inhibitors on the lifespan and healthspan of C. elegans.
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15
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Colón-Bolea P, García-Gómez R, Casar B. RAC1 Activation as a Potential Therapeutic Option in Metastatic Cutaneous Melanoma. Biomolecules 2021; 11:1554. [PMID: 34827551 PMCID: PMC8615836 DOI: 10.3390/biom11111554] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/21/2022] Open
Abstract
Metastasis is a complex process by which cancer cells escape from the primary tumor to colonize distant organs. RAC1 is a member of the RHO family of small guanosine triphosphatases that plays an important role in cancer migration, invasion, angiogenesis and metastasis. RAC1 activation has been related to most cancers, such as cutaneous melanoma, breast, lung, and pancreatic cancer. RAC1P29S driver mutation appears in a significant number of cutaneous melanoma cases. Likewise, RAC1 is overexpressed or hyperactivated via signaling through oncogenic cell surface receptors. Thus, targeting RAC1 represents a promising strategy for cutaneous melanoma therapy, as well as for inhibition of other signaling activation that promotes resistance to targeted therapies. In this review, we focus on the role of RAC1 in metastatic cutaneous melanoma emphasizing the anti-metastatic potential of RAC1- targeting drugs.
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Affiliation(s)
- Paula Colón-Bolea
- Instituto de Biomedicina y Biotecnología de Cantabria, Consejo Superior de Investigaciones Científicas—Universidad de Cantabria, 39011 Santander, Spain; (P.C.-B.); (R.G.-G.)
| | - Rocío García-Gómez
- Instituto de Biomedicina y Biotecnología de Cantabria, Consejo Superior de Investigaciones Científicas—Universidad de Cantabria, 39011 Santander, Spain; (P.C.-B.); (R.G.-G.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Berta Casar
- Instituto de Biomedicina y Biotecnología de Cantabria, Consejo Superior de Investigaciones Científicas—Universidad de Cantabria, 39011 Santander, Spain; (P.C.-B.); (R.G.-G.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
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16
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Biswal J, Jayaprakash P, Rayala SK, Venkatraman G, Rangaswamy R, Jeyaraman J. WaterMap and Molecular Dynamic Simulation-Guided Discovery of Potential PAK1 Inhibitors Using Repurposing Approaches. ACS OMEGA 2021; 6:26829-26845. [PMID: 34693105 PMCID: PMC8529594 DOI: 10.1021/acsomega.1c02032] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Indexed: 06/13/2023]
Abstract
p21-Activated kinase 1 (PAK1) is positioned at the nexus of several oncogenic signaling pathways. Currently, there are no approved inhibitors for disabling the transfer of phosphate in the active site directly, as they are limited by lower affinity, and poor kinase selectivity. In this work, a repurposing study utilizing FDA-approved drugs from the DrugBank database was pursued with an initial selection of 27 molecules out of ∼2162 drug molecules, based on their docking energies and molecular interaction patterns. From the molecules that were considered for WaterMap analysis, seven molecules, namely, Mitoxantrone, Labetalol, Acalabrutinib, Sacubitril, Flubendazole, Trazodone, and Niraparib, ascertained the ability to overlap with high-energy hydration sites. Considering many other displaced unfavorable water molecules, only Acalabrutinib, Flubendazole, and Trazodone molecules highlighted their prominence in terms of binding affinity gains through ΔΔG that ranges between 6.44 and 2.59 kcal/mol. Even if Mitoxantrone exhibited the highest docking score and greater interaction strength, it did not comply with the WaterMap and molecular dynamics simulation results. Moreover, detailed MD simulation trajectory analyses suggested that the drug molecules Flubendazole, Niraparib, and Acalabrutinib were highly stable, observed from their RMSD values and consistent interaction pattern with Glu315, Glu345, Leu347, and Asp407 including the hydrophobic interactions maintained in the three replicates. However, the drug molecule Trazodone displayed a loss of crucial interaction with Leu347, which was essential to inhibit the kinase activity of PAK1. The molecular orbital and electrostatic potential analyses elucidated the reactivity and strong complementarity potentials of the drug molecules in the binding pocket of PAK1. Therefore, the CADD-based reposition efforts, reported in this work, helped in the successful identification of new PAK1 inhibitors that requires further investigation by in vitro analysis.
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Affiliation(s)
- Jayashree Biswal
- Structural
Biology and Bio-Computing Laboratory, Department of Bioinformatics,
Science Block, Alagappa University, Karaikudi 630 004, Tamil Nadu, India
| | - Prajisha Jayaprakash
- Structural
Biology and Bio-Computing Laboratory, Department of Bioinformatics,
Science Block, Alagappa University, Karaikudi 630 004, Tamil Nadu, India
| | - Suresh Kumar Rayala
- Department
of Biotechnology, Indian Institute of Technology
Madras, Room No. BT 306, Chennai 600 036, Tamil Nadu, India
| | - Ganesh Venkatraman
- Department
of Human Genetics, College of Biomedical Sciences, Sri Ramachandra University, Porur, Chennai 600 116, Tamil Nadu, India
| | - Raghu Rangaswamy
- Structural
Biology and Bio-Computing Laboratory, Department of Bioinformatics,
Science Block, Alagappa University, Karaikudi 630 004, Tamil Nadu, India
| | - Jeyakanthan Jeyaraman
- Structural
Biology and Bio-Computing Laboratory, Department of Bioinformatics,
Science Block, Alagappa University, Karaikudi 630 004, Tamil Nadu, India
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17
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Tesch R, Rak M, Raab M, Berger LM, Kronenberger T, Joerger AC, Berger BT, Abdi I, Hanke T, Poso A, Strebhardt K, Sanhaji M, Knapp S. Structure-Based Design of Selective Salt-Inducible Kinase Inhibitors. J Med Chem 2021; 64:8142-8160. [PMID: 34086472 DOI: 10.1021/acs.jmedchem.0c02144] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Salt-inducible kinases (SIKs) are key metabolic regulators. The imbalance in SIK function is associated with the development of diverse cancers, including breast, gastric, and ovarian cancers. Chemical tools to clarify the roles of SIK in different diseases are, however, sparse and are generally characterized by poor kinome-wide selectivity. Here, we have adapted the pyrido[2,3-d]pyrimidin-7-one-based p21-activated kinase (PAK) inhibitor G-5555 for the targeting of SIK, by exploiting differences in the back-pocket region of these kinases. Optimization was supported by high-resolution crystal structures of G-5555 bound to the known off-targets, MST3 and MST4, leading to a chemical probe, MRIA9, with dual SIK/PAK activity and excellent selectivity over other kinases. Furthermore, we show that MRIA9 sensitizes ovarian cancer cells to treatment with the mitotic agent paclitaxel, confirming earlier data from genetic knockdown studies and suggesting a combination therapy with SIK inhibitors and paclitaxel for the treatment of paclitaxel-resistant ovarian cancer.
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Affiliation(s)
- Roberta Tesch
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Marcel Rak
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Monika Raab
- Department of Obstetrics and Gynaecology, School of Medicine, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main 60590, Germany
| | - Lena M Berger
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Thales Kronenberger
- Dept. of Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Str. 14, Tübingen 72076, Germany
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, Kuopio 70210, Finland
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Benedict-Tilman Berger
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Ismahan Abdi
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Thomas Hanke
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Antti Poso
- Dept. of Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Str. 14, Tübingen 72076, Germany
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, Kuopio 70210, Finland
| | - Klaus Strebhardt
- Department of Obstetrics and Gynaecology, School of Medicine, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main 60590, Germany
| | - Mourad Sanhaji
- Department of Obstetrics and Gynaecology, School of Medicine, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main 60590, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
- German Translational Cancer Network (DKTK) and Frankfurt Cancer Institute (FCI), Frankfurt am Main 60438, Germany
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18
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Zhang Y, Pike A. Pyridones in drug discovery: Recent advances. Bioorg Med Chem Lett 2021; 38:127849. [DOI: 10.1016/j.bmcl.2021.127849] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/29/2021] [Accepted: 02/02/2021] [Indexed: 12/17/2022]
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19
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Liu H, Liu K, Dong Z. The Role of p21-Activated Kinases in Cancer and Beyond: Where Are We Heading? Front Cell Dev Biol 2021; 9:641381. [PMID: 33796531 PMCID: PMC8007885 DOI: 10.3389/fcell.2021.641381] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/03/2021] [Indexed: 12/12/2022] Open
Abstract
The p21-activated kinases (PAKs), downstream effectors of Ras-related Rho GTPase Cdc42 and Rac, are serine/threonine kinases. Biologically, PAKs participate in various cellular processes, including growth, apoptosis, mitosis, immune response, motility, inflammation, and gene expression, making PAKs the nexus of several pathogenic and oncogenic signaling pathways. PAKs were proved to play critical roles in human diseases, including cancer, infectious diseases, neurological disorders, diabetes, pancreatic acinar diseases, and cardiac disorders. In this review, we systematically discuss the structure, function, alteration, and molecular mechanisms of PAKs that are involved in the pathogenic and oncogenic effects, as well as PAK inhibitors, which may be developed and deployed in cancer therapy, anti-viral infection, and other diseases. Furthermore, we highlight the critical questions of PAKs in future research, which provide an opportunity to offer input and guidance on new directions for PAKs in pathogenic, oncogenic, and drug discovery research.
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Affiliation(s)
- Hui Liu
- Department of Pathophysiology, School of Basic Medical Sciences, The Academy of Medical Science, College of Medical, Zhengzhou University, Zhengzhou, China
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, The Academy of Medical Science, College of Medical, Zhengzhou University, Zhengzhou, China.,China-US (Henan) Hormel Cancer Institute, Zhengzhou, China
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, The Academy of Medical Science, College of Medical, Zhengzhou University, Zhengzhou, China.,China-US (Henan) Hormel Cancer Institute, Zhengzhou, China
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20
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Xia J, Pei Q, Zheng M, Xie Z. An activatable fluorescent prodrug of paclitaxel and BODIPY. J Mater Chem B 2021; 9:2308-2313. [DOI: 10.1039/d0tb02510k] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A redox-activated paclitaxel prodrug (PTX-S-BDP) was synthesized. PTX-S-BDP NPs were fabricated by the coassembly of PTX-S-BDP with F-127, which can release PTX under redox conditions and exhibit superior cellular imaging and selectivity to cancer cells.
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Affiliation(s)
- Jinxiu Xia
- School of Chemistry and Life Science
- Advanced Institute of Materials Science
- Changchun University of Technology
- 2055 Yanan Street
- Changchun
| | - Qing Pei
- State Key Laboratory of Polymer Physics and Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- 5625 Renmin Street
- Changchun
| | - Min Zheng
- School of Chemistry and Life Science
- Advanced Institute of Materials Science
- Changchun University of Technology
- 2055 Yanan Street
- Changchun
| | - Zhigang Xie
- State Key Laboratory of Polymer Physics and Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- 5625 Renmin Street
- Changchun
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21
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Zhang M, Fang X, Wang C, Hua Y, Huang C, Wang M, Zhu L, Wang Z, Gao Y, Zhang T, Liu H, Zhang Y, Lu S, Lu T, Chen Y, Li H. Design and synthesis of 1H-indazole-3-carboxamide derivatives as potent and selective PAK1 inhibitors with anti-tumour migration and invasion activities. Eur J Med Chem 2020; 203:112517. [DOI: 10.1016/j.ejmech.2020.112517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/15/2020] [Accepted: 05/29/2020] [Indexed: 12/11/2022]
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Yadav P, Shah K. An overview on synthetic and pharmaceutical prospective of pyrido[2,3-d]pyrimidines scaffold. Chem Biol Drug Des 2020; 97:633-648. [PMID: 32946161 DOI: 10.1111/cbdd.13800] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/30/2020] [Accepted: 09/03/2020] [Indexed: 12/26/2022]
Abstract
Pyrido[2,3-d]pyrimidine, a fused hetero-bicyclic nucleus containing pyridine and pyrimidine rings has attained the momentary attention in the sphere of multicomponent synthetic protocol and medicinal chemist. Pyrido[2,3-d]pyrimidine derived drugs have manifested diverse pharmacological activities, particularly, anti-inflammatory, cytotoxic, antimicrobial, phosphodiesterase inhibitors and cytokine inhibitors etc. The present review illustrates various modern synthetic strategies adopted, the structure-activity relationship (SAR) aspects and discloses the extensive crucial biological properties (anticancer, anti-infectious, anti-diabetics and CNS agents) of pyrido[2,3-d]pyrimidines.
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Affiliation(s)
- Pratibha Yadav
- Institute of Pharmaceutical Research, GLA University, Mathura, UP, India
| | - Kamal Shah
- Institute of Pharmaceutical Research, GLA University, Mathura, UP, India
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Coordinated dysregulation of cancer progression by the HER family and p21-activated kinases. Cancer Metastasis Rev 2020; 39:583-601. [PMID: 32820388 DOI: 10.1007/s10555-020-09922-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 07/25/2020] [Indexed: 12/20/2022]
Abstract
Most epithelial cancer types are polygenic in nature and are driven by coordinated dysregulation of multiple regulatory pathways, genes, and protein modifications. The process of coordinated regulation of cancer promoting pathways in response to extrinsic and intrinsic signals facilitates the dysregulation of several pathways with complementary functions, contributing to the hallmarks of cancer. Dysregulation and hyperactivation of cell surface human epidermal growth factor receptors (HERs) and cytoskeleton remodeling by p21-activated kinases (PAKs) are two prominent interconnected aspects of oncogenesis. We briefly discuss the discoveries and significant advances in the area of coordinated regulation of HERs and PAKs in the development and progression of breast and other epithelial cancers. We also discuss how initial studies involving heregulin signaling via HER3-HER2 axis and HER2-overexpressing breast cancer cells not only discovered a mechanistic role of PAK1 in breast cancer pathobiology but also acted as a bridge in generating a broader cancer research interest in other PAK family members and cancer types and catalyzed establishing the role of PAKs in human cancer, at-large. In addition, growth factor stimulation of the PAK pathway also helped to recognize new facets of PAKs, connecting the PAK pathway to oncogenesis, nuclear signaling, gene expression, mitotic progression, DNA damage response, among other phenotypic responses, and shaped the field of PAK cancer research. Finally, we recount some of the current limitations of HER- and PAK-directed therapeutics in counteracting acquired therapeutic resistance and discuss how cancer's as a polygenic disease may be best targeted with a polygenic approach.
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Yao D, Li C, Rajoka MSR, He Z, Huang J, Wang J, Zhang J. P21-Activated Kinase 1: Emerging biological functions and potential therapeutic targets in Cancer. Am J Cancer Res 2020; 10:9741-9766. [PMID: 32863957 PMCID: PMC7449905 DOI: 10.7150/thno.46913] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 07/23/2020] [Indexed: 02/06/2023] Open
Abstract
The p21-Activated kinase 1 (PAK1), a member of serine-threonine kinases family, was initially identified as an interactor of the Rho GTPases RAC1 and CDC42, which affect a wide range of processes associated with cell motility, survival, metabolism, cell cycle, proliferation, transformation, stress, inflammation, and gene expression. Recently, the PAK1 has emerged as a potential therapeutic target in cancer due to its role in many oncogenic signaling pathways. Many PAK1 inhibitors have been developed as potential preclinical agents for cancer therapy. Here, we provide an overview of essential roles that PAK1 plays in cancer, including its structure and autoactivation mechanism, its crucial function from onset to progression to metastasis, metabolism, immune escape and even drug resistance in cancer; endogenous regulators; and cancer-related pathways. We also summarize the reported PAK1 small-molecule inhibitors based on their structure types and their potential application in cancer. In addition, we provide overviews on current progress and future challenges of PAK1 in cancer, hoping to provide new ideas for the diagnosis and treatment of cancer.
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Qin Q, Wu T, Yin W, Sun Y, Zhang X, Wang R, Guo J, Zhao D, Cheng M. Discovery of 2,4-diaminopyrimidine derivatives targeting p21-activated kinase 4: Biological evaluation and docking studies. Arch Pharm (Weinheim) 2020; 353:e2000097. [PMID: 32627873 DOI: 10.1002/ardp.202000097] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 01/05/2023]
Abstract
In this study, novel 2,4-diaminopyrimidine derivatives targeting p21-activated kinase 4 (PAK4) were discovered and evaluated for their biological activity against PAK4. Among the derivatives studied, promising compounds A2, B6, and B8 displayed the highest inhibitory activities against PAK4 (IC50 = 18.4, 5.9, and 20.4 nM, respectively). From the cellular assay, compound B6 exhibited the highest potency with an IC50 value of 2.533 μM against A549 cells. Some compounds were selected for computational ADME (absorption, distribution, metabolism, and elimination) properties and molecular docking studies against PAK4. The detailed structure-activity relationship based on the biochemical activities and molecular docking studies were explored. According to the docking studies, compound B6 had the lowest docking score (docking energy: -7.593 kcal/mol). The molecular docking simulation indicated the binding mode between compound B6 and PAK4. All these results suggest compound B6 as a useful candidate for the development of a PAK4 inhibitor.
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Affiliation(s)
- Qiaohua Qin
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Tianxiao Wu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Wenbo Yin
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Yixiang Sun
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Xiangyu Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Ruifeng Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Jing Guo
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
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RAC1 as a Therapeutic Target in Malignant Melanoma. Trends Cancer 2020; 6:478-488. [PMID: 32460002 DOI: 10.1016/j.trecan.2020.02.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/19/2020] [Accepted: 02/26/2020] [Indexed: 12/22/2022]
Abstract
Small GTPases of the RAS and RHO families are related signaling proteins that, when activated by growth factors or by mutation, drive oncogenic processes. While activating mutations in KRAS, NRAS, and HRAS genes have long been recognized and occur in many types of cancer, similar mutations in RHO family genes, such as RAC1 and RHOA, have only recently been detected as the result of extensive cancer genome-sequencing efforts and are linked to a restricted set of malignancies. In this review, we focus on the role of RAC1 signaling in malignant melanoma, emphasizing recent advances that describe how this oncoprotein alters melanocyte proliferation and motility and how these findings might lead to new therapeutics in RAC1-mutant tumors.
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Computational insight into the mechanisms of action and selectivity of Afraxis PAK inhibitors. Future Med Chem 2020; 12:367-385. [PMID: 32064922 DOI: 10.4155/fmc-2019-0273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Aim: The p21-activated kinases (PAKs) are involved in many important biological activity regulations. FRAX019, FRAX414, FRAX597, FRAX1036 and G-5555 were identified as PAKs inhibitors. Their detailed inhibitory mechanisms deserve further investigation. Results: Molecular dynamics simulations and further calculations for the PAK1/inhibitor and PAK4/inhibitor complexes indicate that their binding free energies are basically consistent with the trend of experimental activity data. Conclusion: The anchoring of residues Leu347PAK1 and Leu398PAK4 is the structural basis for designing Afraxis PAK inhibitors. This study discloses the inhibitory mechanisms of FRAX019, FRAX414, FRAX597, FRAX1036 and G-5555 toward PAK1 and PAK4 and some clues to enhance kinase activities and selectivities, which will provide valuable information to the development of more potent and selective PAK inhibitors.
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Pyrido[2,3- d]pyrimidin-7(8 H)-ones: Synthesis and Biomedical Applications. Molecules 2019; 24:molecules24224161. [PMID: 31744155 PMCID: PMC6891647 DOI: 10.3390/molecules24224161] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 12/20/2022] Open
Abstract
Pyrido[2,3-d]pyrimidines (1) are a type of privileged heterocyclic scaffolds capable of providing ligands for several receptors in the body. Among such structures, our group and others have been particularly interested in pyrido[2,3-d]pyrimidine-7(8H)-ones (2) due to the similitude with nitrogen bases present in DNA and RNA. Currently there are more than 20,000 structures 2 described which correspond to around 2900 references (half of them being patents). Furthermore, the number of references containing compounds of general structure 2 have increased almost exponentially in the last 10 years. The present review covers the synthetic methods used for the synthesis of pyrido[2,3-d]pyrimidine-7(8H)-ones (2), both starting from a preformed pyrimidine ring or a pyridine ring, and the biomedical applications of such compounds.
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Guo J, Wang T, Wu T, Zhang K, Yin W, Zhu M, Pang Y, Hao C, He Z, Cheng M, Liu Y, Zheng J, Gu J, Zhao D. Synthesis, bioconversion, pharmacokinetic and pharmacodynamic evaluation of N-isopropyl-oxy-carbonyloxymethyl prodrugs of CZh-226, a potent and selective PAK4 inhibitor. Eur J Med Chem 2019; 186:111878. [PMID: 31757524 DOI: 10.1016/j.ejmech.2019.111878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/11/2019] [Accepted: 11/11/2019] [Indexed: 12/12/2022]
Abstract
We have previously disclosed compound 3 (CZh-226), a potent and selective PAK4 inhibitor, but its development was delayed due to poor oral pharmacokinetics. In an attempt to improve this issue, we synthesised a series of prodrugs by masking its terminal nitrogen of the piperazine moiety. Most synthesised prodrugs of 3 have low or no inhibition of PAK4 activity. The stability of synthetic prodrugs was evaluated in PBS, SGF, SIF, rat plasma and liver S9 fraction. Of these, prodrug 19 was not only stable under both acidic and neutral conditions but also could be quickly converted to parent drug 3 in rat plasma and liver S9 fraction. Such effective conversion into parent drug 3 was observed in rats, providing higher exposure of 3 compared to its direct administration. When given via oral route at daily doses of 25 and 50 mg/kg, the prodrug 19 was effective and well tolerated in mouse model of HCT-116 and B16F10.
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Affiliation(s)
- Jing Guo
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Tingting Wang
- Research Institute of Translational Medicine, The First Bethune Hospital of Jilin University, Changchun, 130061, China; Research Center for Drug Metabolism, College of Life Science, Jilin University, Changchun, 130012, China
| | - Tianxiao Wu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Kehan Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
| | - Wenbo Yin
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Mingyue Zhu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yu Pang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Chenzhou Hao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Zhonggui He
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yang Liu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Jiang Zheng
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China; State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, 550025, China
| | - Jingkai Gu
- Research Institute of Translational Medicine, The First Bethune Hospital of Jilin University, Changchun, 130061, China; Research Center for Drug Metabolism, College of Life Science, Jilin University, Changchun, 130012, China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China.
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Song PL, Wang G, Su Y, Wang HX, Wang J, Li F, Cheng MS. Strategy and validation of a structure-based method for the discovery of selective inhibitors of PAK isoforms and the evaluation of their anti-cancer activity. Bioorg Chem 2019; 91:103168. [DOI: 10.1016/j.bioorg.2019.103168] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 07/29/2019] [Accepted: 07/29/2019] [Indexed: 02/07/2023]
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Wang H, Gao Y, Wang J, Cheng M. Computational Strategy Revealing the Structural Determinant of Ligand Selectivity towards Highly Similar Protein Targets. Curr Drug Targets 2019; 21:76-88. [PMID: 31556854 DOI: 10.2174/1389450120666190926113524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 08/27/2019] [Accepted: 08/27/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Poor selectivity of drug candidates may lead to toxicity and side effects accounting for as high as 60% failure rate, thus, the selectivity is consistently significant and challenging for drug discovery. OBJECTIVE To find highly specific small molecules towards very similar protein targets, multiple strategies are always employed, including (1) To make use of the diverse shape of binding pocket to avoid steric bump; (2) To increase binding affinities for favorite residues; (3) To achieve selectivity through allosteric regulation of target; (4) To stabalize the inactive conformation of protein target and (5) To occupy dual binding pockets of single target. CONCLUSION In this review, we summarize computational strategies along with examples of their successful applications in designing selective ligands, with the aim to provide insights into everdiversifying drug development practice and inspire medicinal chemists to utilize computational strategies to avoid potential side effects due to low selectivity of ligands.
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Affiliation(s)
- Hanxun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
| | - Yinli Gao
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
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Su Y, Song P, Wang H, Hu B, Wang J, Cheng MS. Precise design of highly isoform-selective p21-activated kinase 4 inhibitors: computational insights into the selectivity mechanism through molecular dynamics simulation and binding free energy calculation. J Biomol Struct Dyn 2019; 38:3825-3837. [DOI: 10.1080/07391102.2019.1664330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yuan Su
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| | - Peilu Song
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| | - Hanxun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| | - Baichun Hu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
| | - Mao-Sheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang PR China
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Knippler CM, Saji M, Rajan N, Porter K, La Perle KMD, Ringel MD. MAPK- and AKT-activated thyroid cancers are sensitive to group I PAK inhibition. Endocr Relat Cancer 2019; 26:699-712. [PMID: 31146260 PMCID: PMC7062234 DOI: 10.1530/erc-19-0188] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 12/25/2022]
Abstract
The number of individuals who succumb to thyroid cancer has been increasing and those who are refractory to standard care have limited therapeutic options, highlighting the importance of developing new treatments for patients with aggressive forms of the disease. Mutational activation of MAPK signaling, through BRAF and RAS mutations and/or gene rearrangements, and activation of PI3K signaling, through mutational activation of PIK3CA or loss of PTEN, are well described in aggressive thyroid cancer. We previously reported overactivation and overexpression of p21-activated kinases (PAKs) in aggressive human thyroid cancer invasive fronts and determined that PAK1 functionally regulated thyroid cancer cell migration. We reported mechanistic crosstalk between the MAPK and PAK pathways that are BRAF-dependent but MEK independent, suggesting that PAK and MEK inhibition might be synergistic. In the present study, we tested this hypothesis. Pharmacologic inhibition of group I PAKs using two PAK kinase inhibitors, G-5555 or FRAX1036, reduced thyroid cancer cell viability, cell cycle progression and migration and invasion, with greater potency for G-5555. Combination of G-5555 with vemurafenib was synergistic in BRAFV600E-mutated thyroid cancer cell lines. Finally, G-5555 restrained thyroid size of BRAFV600E-driven murine papillary thyroid cancer by >50% (P < 0.0001) and reduced carcinoma formation (P = 0.0167), despite maintenance of MAPK activity. Taken together, these findings suggest both that group I PAKs may be a new therapeutic target for thyroid cancer and that PAK activation is functionally important for BRAFV600E-mediated thyroid cancer development.
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Affiliation(s)
- Christina M. Knippler
- Division of Endocrinology, Diabetes, and Metabolism, The Ohio State University Wexner Medical Center and Arthur G. James Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Motoyasu Saji
- Division of Endocrinology, Diabetes, and Metabolism, The Ohio State University Wexner Medical Center and Arthur G. James Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Neel Rajan
- College of Arts and Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Kyle Porter
- Center for Biostatistics, Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
| | - Krista M. D. La Perle
- Department of Veterinary Biosciences, Comparative Pathology & Mouse Phenotyping Shared Resource, The Ohio State University, Columbus, Ohio, USA
| | - Matthew D. Ringel
- Division of Endocrinology, Diabetes, and Metabolism, The Ohio State University Wexner Medical Center and Arthur G. James Comprehensive Cancer Center, Columbus, Ohio, USA
- To whom correspondence should be addressed: Matthew D. Ringel, MD, Ralph W. Kurtz Professor of Medicine, Director, Division of Endocrinology, Diabetes, and Metabolism, The Ohio State University College of Medicine & Comprehensive Cancer Center, McCampbell Hall, Room 565, 1581 Dodd Drive, Columbus, OH 43210, Tel: 614-685-3333,
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Solution structures and biophysical analysis of full-length group A PAKs reveal they are monomeric and auto-inhibited in cis. Biochem J 2019; 476:1037-1051. [PMID: 30858169 PMCID: PMC6448136 DOI: 10.1042/bcj20180867] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 03/05/2019] [Accepted: 03/08/2019] [Indexed: 12/13/2022]
Abstract
The group A p21-activated kinases (PAKs) exist in an auto-inhibited form until activated by GTPase binding and auto-phosphorylation. In the auto-inhibited form, a regulatory domain binds to the kinase domain (KD) blocking the binding of substrates, and CDC42 or Rac binding to the regulatory domain relieves this auto-inhibition allowing auto-phosphorylation on the KD activation loop. We have determined the crystal structure of the PAK3 catalytic domain and by small angle X-ray scattering, the solution-phase structures of full-length inactive PAK1 and PAK3. The structures reveal a compact but elongated molecular shape that demonstrates that, together with multiple independent biophysical measurements and in contrast with previous assumptions, group A PAKs are monomeric both before and after activation, consistent with an activation mechanism of cis-auto-inhibition and initial cis-auto-phosphorylation, followed by transient dimerisation to allow trans-auto-phosphorylation for full activation, yielding a monomeric active PAK protein.
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Chung EY, Mai Y, Shah UA, Wei Y, Ishida E, Kataoka K, Ren X, Pradhan K, Bartholdy B, Wei X, Zou Y, Zhang J, Ogawa S, Steidl U, Zang X, Verma A, Janakiram M, Ye BH. PAK Kinase Inhibition Has Therapeutic Activity in Novel Preclinical Models of Adult T-Cell Leukemia/Lymphoma. Clin Cancer Res 2019; 25:3589-3601. [PMID: 30862694 DOI: 10.1158/1078-0432.ccr-18-3033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/11/2019] [Accepted: 03/06/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE To evaluate therapeutic activity of PAK inhibition in ATLL and to characterize the role of PAK isoforms in cell proliferation, survival, and adhesion of ATLL cells in preclinical models. EXPERIMENTAL DESIGN Frequency and prognostic impact of PAK2 amplification were evaluated in an ATLL cohort of 370 cases. Novel long-term cultures and in vivo xenograft models were developed using primary ATLL cells from North American patients. Two PAK inhibitors were used to block PAK kinase activity pharmacologically. siRNA-based gene silencing approach was used to genetically knockdown (KD) PAK1 and PAK2 in ATLL cell lines. RESULTS PAK1/2/4 are the three most abundantly expressed PAK family members in ATLL. PAK2 amplifications are seen in 24% of ATLLs and are associated with worse prognosis in a large patient cohort. The pan-PAK inhibitor PF-3758309 (PF) has strong in vitro and in vivo activity in a variety of ATLL preclinical models. These activities of PF are likely attributed to its ability to target several PAK isoforms simultaneously because genetic silencing of either PAK1 or PAK2 produced more modest effects. PAK2 plays a major role in CADM1-mediated stromal interaction, which is an important step in systemic dissemination of the disease. This finding is consistent with the observation that PAK2 amplification is more frequent in aggressive ATLLs and correlates with inferior outcome. CONCLUSIONS PAK2, a gene frequently amplified in ATLL, facilitates CADM1-mediated stromal interaction and promotes survival of ATLL cells. Taken together, PAK inhibition may hold significant promise as a targeted therapy for aggressive ATLLs.
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Affiliation(s)
- Elaine Y Chung
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York
| | - Yun Mai
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York
| | - Urvi A Shah
- Department of Oncology, Montefiore Medical Center, Bronx, New York
| | - Yongqiang Wei
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York.,Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Elise Ishida
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Xiaoxin Ren
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York
| | - Kith Pradhan
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York
| | - Boris Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York
| | - Xiaolei Wei
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York.,Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yiyu Zou
- Department of Oncology, Montefiore Medical Center, Bronx, New York
| | - Jinghang Zhang
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Ulrich Steidl
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York
| | - Xingxing Zang
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York
| | - Amit Verma
- Department of Oncology, Montefiore Medical Center, Bronx, New York.,Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York
| | - Murali Janakiram
- Department of Oncology, Montefiore Medical Center, Bronx, New York
| | - B Hilda Ye
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York.
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Molosh AI, Shekhar A. Neurofibromatosis type 1 as a model system to study molecular mechanisms of autism spectrum disorder symptoms. PROGRESS IN BRAIN RESEARCH 2018; 241:37-62. [PMID: 30447756 DOI: 10.1016/bs.pbr.2018.09.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Neurofibromatosis type 1 (NF1) is monogenic neurodevelopmental disorder caused by mutation of NF1 gene, which leads to increased susceptibility to various tumors formations. Additionally, majority of patients with NF1 are experience high incidence of cognitive deficits. Particularly, we review the growing number of reports demonstrated a higher incidence of autism spectrum disorder (ASD) in individuals with NF1. In this review we also discuss face validity of preclinical Nf1 mouse models. Then we describe discoveries from these animal models that have uncovered the deficiencies in the regulation of Ras and other intracellular pathways as critical mechanisms underlying the Nf1 cognitive problems. We also summarize and interpret recent preclinical and clinical studies that point toward potential pharmacological therapies for NF1 patients.
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Affiliation(s)
- Andrei I Molosh
- Department of Psychiatry, Institute of Psychiatric Research, IU School of Medicine, Indianapolis, IN, United States; Stark Neurosciences Research Institute, IU School of Medicine, Indianapolis, IN, United States.
| | - Anantha Shekhar
- Department of Psychiatry, Institute of Psychiatric Research, IU School of Medicine, Indianapolis, IN, United States; Stark Neurosciences Research Institute, IU School of Medicine, Indianapolis, IN, United States; Department of Pharmacology & Toxicology, IU School of Medicine, Indianapolis, IN, United States; Indiana Clinical and Translational Institute, IU School of Medicine, Indianapolis, IN, United States
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37
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Chow HY, Dong B, Valencia CA, Zeng CT, Koch JN, Prudnikova TY, Chernoff J. Group I Paks are essential for epithelial- mesenchymal transition in an Apc-driven model of colorectal cancer. Nat Commun 2018; 9:3473. [PMID: 30150766 PMCID: PMC6110733 DOI: 10.1038/s41467-018-05935-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 08/02/2018] [Indexed: 02/05/2023] Open
Abstract
p21-activated kinases (Paks) play an important role in oncogenic signaling pathways and have been considered as potential therapeutic targets in various cancers. Most studies of Pak function employ gene knock-out or knock-down methods, but these approaches result in loss of both enzymatic and scaffolding properties of these proteins, and thus may not reflect the effects of small molecule inhibitors. Here we use a transgenic mouse model in which a specific peptide inhibitor of Group I Paks is conditionally expressed in response to Cre recombinase. Using this model, we show that inhibition of endogenous Paks impedes the transition of adenoma to carcinoma in an Apc-driven mouse model of colorectal cancer. These effects are mediated by inhibition of Wnt signaling through reduced β-catenin activity as well as suppression of an epithelial-mesenchymal transition program mediated by miR-200 and Snai1. These results highlight the potential therapeutic role of Pak1 inhibitors in colorectal cancer.
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Affiliation(s)
- H Y Chow
- Cancer Center, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, 610041, Chengdu, Sichuan, China
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - B Dong
- Cancer Center, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, 610041, Chengdu, Sichuan, China
| | - C A Valencia
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - C T Zeng
- Cancer Center, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, 610041, Chengdu, Sichuan, China
| | - J N Koch
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - T Y Prudnikova
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - J Chernoff
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
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Discovery of 2-(4-Substituted-piperidin/piperazine-1-yl)-N-(5-cyclopropyl-1H-pyrazol-3-yl)-quinazoline-2,4-diamines as PAK4 Inhibitors with Potent A549 Cell Proliferation, Migration, and Invasion Inhibition Activity. Molecules 2018; 23:molecules23020417. [PMID: 29443911 PMCID: PMC6100240 DOI: 10.3390/molecules23020417] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 02/08/2018] [Accepted: 02/11/2018] [Indexed: 02/07/2023] Open
Abstract
A series of novel 2,4-diaminoquinazoline derivatives were designed, synthesized, and evaluated as p21-activated kinase 4 (PAK4) inhibitors. All compounds showed significant inhibitory activity against PAK4 (half-maximal inhibitory concentration IC50 < 1 μM). Among them, compounds 8d and 9c demonstrated the most potent inhibitory activity against PAK4 (IC50 = 0.060 μM and 0.068 μM, respectively). Furthermore, we observed that compounds 8d and 9c displayed potent antiproliferative activity against the A549 cell line and inhibited cell cycle distribution, migration, and invasion of this cell line. In addition, molecular docking analysis was performed to predict the possible binding mode of compound 8d. This series of compounds has the potential for further development as PAK4 inhibitors for anticancer activity.
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Hao C, Zhao F, Song H, Guo J, Li X, Jiang X, Huan R, Song S, Zhang Q, Wang R, Wang K, Pang Y, Liu T, Lu T, Huang W, Wang J, Lin B, He Z, Li H, Li F, Zhao D, Cheng M. Structure-Based Design of 6-Chloro-4-aminoquinazoline-2-carboxamide Derivatives as Potent and Selective p21-Activated Kinase 4 (PAK4) Inhibitors. J Med Chem 2017; 61:265-285. [PMID: 29190083 DOI: 10.1021/acs.jmedchem.7b01342] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Herein, we report the discovery and characterization of a novel class of PAK4 inhibitors with a quinazoline scaffold. Based on the shape and chemical composition of the ATP-binding pocket of PAKs, we chose a 2,4-diaminoquinazoline series of inhibitors as a starting point. Guided by X-ray crystallography and a structure-based drug design (SBDD) approach, a series of novel 4-aminoquinazoline-2-carboxamide PAK4 inhibitors were designed and synthesized. The inhibitors' selectivity, therapeutic potency, and pharmaceutical properties were optimized. One of the best compounds, 31 (CZh226), showed remarkable PAK4 selectivity (346-fold vs PAK1) and favorable kinase selectivity profile. Moreover, this compound potently inhibited the migration and invasion of A549 tumor cells by regulating the PAK4-directed downstream signaling pathways in vitro. Taken together, these data support the further development of 31 as a lead compound for PAK4-targeted anticancer drug discovery and as a valuable research probe for the further biological investigation of group II PAKs.
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Affiliation(s)
- Chenzhou Hao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University , Shenyang 110016, China
| | - Fan Zhao
- Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University , Beijing 100084, China
| | - Hongyan Song
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research) , 2 Fusionopolis Way, Innovis, #08-03, Singapore 138634
| | - Jing Guo
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University , Shenyang 110016, China
| | - Xiaodong Li
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University , Shenyang 110001, China
| | - Xiaolin Jiang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University , Shenyang 110016, China
| | - Ran Huan
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University , Shenyang 110001, China
| | - Shuai Song
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University , Shenyang 110016, China
| | - Qiaoling Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University , Shenyang 110016, China
| | - Ruifeng Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University , Shenyang 110016, China
| | - Kai Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University , Shenyang 110016, China
| | - Yu Pang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University , Shenyang 110016, China
| | - Tongchao Liu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University , Shenyang 110016, China
| | - Tianqi Lu
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University , Shenyang 110001, China
| | - Wanxu Huang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University , Shenyang 110016, China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University , Shenyang 110016, China
| | - Bin Lin
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University , Shenyang 110016, China
| | - Zhonggui He
- School of Pharmacy, Shenyang Pharmaceutical University , Shenyang 110016, China
| | - Haitao Li
- Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University , Beijing 100084, China
| | - Feng Li
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University , Shenyang 110001, China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University , Shenyang 110016, China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University , Shenyang 110016, China
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Abstract
Malignant carcinomas are often characterized by metastasis, the movement of carcinoma cells from a primary site to colonize distant organs. For metastasis to occur, carcinoma cells first must adopt a pro-migratory phenotype and move through the surrounding stroma towards a blood or lymphatic vessel. Currently, there are very limited possibilities to target these processes therapeutically. The family of Rho GTPases is an ubiquitously expressed division of GTP-binding proteins involved in the regulation of cytoskeletal dynamics and intracellular signaling. The best characterized members of the Rho family GTPases are RhoA, Rac1 and Cdc42. Abnormalities in Rho GTPase function have major consequences for cancer progression. Rho GTPase activation is driven by cell surface receptors that activate GTP exchange factors (GEFs) and GTPase-activating proteins (GAPs). In this review, we summarize our current knowledge on Rho GTPase function in the regulation of metastasis. We will focus on key discoveries in the regulation of epithelial-mesenchymal-transition (EMT), cell-cell junctions, formation of membrane protrusions, plasticity of cell migration and adaptation to a hypoxic environment. In addition, we will emphasize on crosstalk between Rho GTPase family members and other important oncogenic pathways, such as cyclic AMP-mediated signaling, canonical Wnt/β-catenin, Yes-associated protein (YAP) and hypoxia inducible factor 1α (Hif1α) and provide an overview of the advancements and challenges in developing pharmacological tools to target Rho GTPase and the aforementioned crosstalk in the context of cancer therapeutics.
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Abstract
p21-Activated kinase 1 (PAK1) has attracted much attention as a potential therapeutic target due to its central role in many oncogenic signaling pathways, its frequent dysregulation in cancers and neurological disorders, and its tractability as a target for small-molecule inhibition. To date, several PAK1-targeting compounds have been developed as preclinical agents, including one that has been evaluated in a clinical trial. A series of ATP-competitive inhibitors, allosteric inhibitors and peptide inhibitors with distinct biochemical and pharmacokinetic properties represent useful laboratory tools for studies on the role of PAK1 in biology and in disease contexts, and could lead to promising therapeutic agents. Given the central role of PAK1 in vital signaling pathways, future clinical development of PAK1 inhibitors will require careful investigation of their safety and efficacy.
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Guo J, Zhu M, Wu T, Hao C, Wang K, Yan Z, Huang W, Wang J, Zhao D, Cheng M. Discovery of indolin-2-one derivatives as potent PAK4 inhibitors: Structure-activity relationship analysis, biological evaluation and molecular docking study. Bioorg Med Chem 2017; 25:3500-3511. [DOI: 10.1016/j.bmc.2017.04.047] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 01/05/2023]
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Current nonclinical testing paradigms in support of safe clinical trials: An IQ Consortium DruSafe perspective. Regul Toxicol Pharmacol 2017; 87 Suppl 3:S1-S15. [PMID: 28483710 DOI: 10.1016/j.yrtph.2017.05.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 12/18/2022]
Abstract
The transition from nonclinical to First-in-Human (FIH) testing is one of the most challenging steps in drug development. In response to serious outcomes in a recent Phase 1 trial (sponsored by Bial), IQ Consortium/DruSafe member companies reviewed their nonclinical approach to progress small molecules safely to FIH trials. As a common practice, safety evaluation begins with target selection and continues through iterative in silico and in vitro screening to identify molecules with increased probability of acceptable in vivo safety profiles. High attrition routinely occurs during this phase. In vivo exploratory and pivotal FIH-enabling toxicity studies are then conducted to identify molecules with a favorable benefit-risk profile for humans. The recent serious incident has reemphasized the importance of nonclinical testing plans that are customized to the target, the molecule, and the intended clinical plan. Despite the challenges and inherent risks of transitioning from nonclinical to clinical testing, Phase 1 studies have a remarkably good safety record. Given the rapid scientific evolution of safety evaluation, testing paradigms and regulatory guidance must evolve with emerging science. The authors posit that the practices described herein, together with science-based risk assessment and management, support safe FIH trials while advancing development of important new medicines.
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John Von Freyend S, Kwok-Schuelein T, Netter HJ, Haqshenas G, Semblat JP, Doerig C. Subverting Host Cell P21-Activated Kinase: A Case of Convergent Evolution across Pathogens. Pathogens 2017; 6:pathogens6020017. [PMID: 28430160 PMCID: PMC5488651 DOI: 10.3390/pathogens6020017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/29/2017] [Accepted: 04/09/2017] [Indexed: 12/14/2022] Open
Abstract
Intracellular pathogens have evolved a wide range of strategies to not only escape from the immune systems of their hosts, but also to directly exploit a variety of host factors to facilitate the infection process. One such strategy is to subvert host cell signalling pathways to the advantage of the pathogen. Recent research has highlighted that the human serine/threonine kinase PAK, or p21-activated kinase, is a central component of host-pathogen interactions in many infection systems involving viruses, bacteria, and eukaryotic pathogens. PAK paralogues are found in most mammalian tissues, where they play vital roles in a wide range of functions. The role of PAKs in cell proliferation and survival, and their involvement in a number of cancers, is of great interest in the context of drug discovery. In this review we discuss the latest insights into the surprisingly central role human PAK1 plays for the infection by such different infectious disease agents as viruses, bacteria, and parasitic protists. It is our intention to open serious discussion on the applicability of PAK inhibitors for the treatment, not only of neoplastic diseases, which is currently the primary objective of drug discovery research targeting these enzymes, but also of a wide range of infectious diseases.
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Affiliation(s)
- Simona John Von Freyend
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia.
| | - Terry Kwok-Schuelein
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia.
- Cancer Program, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia.
| | - Hans J Netter
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia.
- Victorian Infectious Diseases Reference Laboratory, Melbourne Health, The Peter Doherty Institute, Melbourne, Victoria 3000, Australia.
| | - Gholamreza Haqshenas
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia.
| | | | - Christian Doerig
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia.
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McCoull W, Hennessy EJ, Blades K, Chuaqui C, Dowling JE, Ferguson AD, Goldberg FW, Howe N, Jones CR, Kemmitt PD, Lamont G, Varnes JG, Ward RA, Yang B. Optimization of Highly Kinase Selective Bis-anilino Pyrimidine PAK1 Inhibitors. ACS Med Chem Lett 2016; 7:1118-1123. [PMID: 27994749 DOI: 10.1021/acsmedchemlett.6b00322] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 09/14/2016] [Indexed: 12/26/2022] Open
Abstract
Group I p21-activated kinase (PAK) inhibitors are indicated as important in cancer progression, but achieving high kinase selectivity has been challenging. A bis-anilino pyrimidine PAK1 inhibitor was identified and optimized through structure-based drug design to improve PAK1 potency and achieve high kinase selectivity, giving in vitro probe compound AZ13705339 (18). Reduction of lipophilicity to lower clearance afforded AZ13711265 (14) as an in vivo probe compound with oral exposure in mouse. Such probes will allow further investigation of PAK1 biology.
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Affiliation(s)
- William McCoull
- AstraZeneca, 310 Cambridge Science Park, Milton
Road, Cambridge, CB4 0WG, U.K
| | - Edward J. Hennessy
- AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Kevin Blades
- AstraZeneca, Alderley Park,
Macclesfield, Cheshire, SK10 4TG, U.K
| | - Claudio Chuaqui
- AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - James E. Dowling
- AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Andrew D. Ferguson
- AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | | | - Nicholas Howe
- AstraZeneca, Alderley Park,
Macclesfield, Cheshire, SK10 4TG, U.K
| | | | - Paul D. Kemmitt
- AstraZeneca, 310 Cambridge Science Park, Milton
Road, Cambridge, CB4 0WG, U.K
| | - Gillian Lamont
- AstraZeneca, 310 Cambridge Science Park, Milton
Road, Cambridge, CB4 0WG, U.K
| | - Jeffrey G. Varnes
- AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Richard A. Ward
- AstraZeneca, 310 Cambridge Science Park, Milton
Road, Cambridge, CB4 0WG, U.K
| | - Bin Yang
- AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
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Prudnikova TY, Chernoff J. The Group I Pak inhibitor Frax-1036 sensitizes 11q13-amplified ovarian cancer cells to the cytotoxic effects of Rottlerin. Small GTPases 2016; 8:193-198. [PMID: 27427770 DOI: 10.1080/21541248.2016.1213089] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The p21-activated kinases (PAKs) are Cdc42/Rac-activated serine-threonine protein kinases that regulate several key cancer-relevant signaling pathways, such as the Mek/Erk, PI3K/Akt, and Wnt/β-catenin cascades. Pak1 is frequently overexpressed and/or hyperactivated in different human cancers, including breast, ovary, prostate, and brain cancer. PAK1 genomic amplification at 11q13 is the most common mechanism of Pak1 hyperactivation, though Pak1 mRNA and/or protein may be overexpressed in the absence of gene amplification. In previous in vitro and in vivo studies we have shown that ovarian cancer cells with amplified/overexpressed Pak1 were significantly more sensitive to pharmacologic inhibition of Pak1 compared to cells without 11q13 amplification. In the present study we examined if additional signaling pathways might be targeted in tandem with the Group I Pak inhibitor Frax-1036 in ovarian cancer cells. Using the ICCB Known Bioactives Library, we found that the cytotoxic effect of Frax-1036 was significantly higher in combination with the PKCδ inhibitor, Rottlerin, suggesting that Pak inhibitors might be combined with other agents to treat 11q13-amplified ovarian cancer.
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Affiliation(s)
| | - Jonathan Chernoff
- a Cancer Biology Program, Fox Chase Cancer Center , Philadelphia , PA , USA
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