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Zhong Z, Wang T, Zang R, Zang Y, Feng Y, Yan S, Geng C, Zhu N, Wang Q. Dual PI3K/mTOR inhibitor PF-04979064 regulates tumor growth in gastric cancer and enhances drug sensitivity of gastric cancer cells to 5-FU. Biomed Pharmacother 2024; 170:116086. [PMID: 38159377 DOI: 10.1016/j.biopha.2023.116086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/19/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024] Open
Abstract
Gastric cancer (GC) is characterized by high tumor heterogeneity, increased surgical difficulty, and limited chemotherapy efficacy, and it is associated with a poor prognosis. The abnormal proliferation of cells involves abnormal activation of the PI3K/AKT/mTOR signaling pathway. Inhibition of this signaling pathway can inhibit tumor cell proliferation and induce cell apoptosis. This study evaluated the effect of PF-04979064, a dual inhibitor of PI3K and mTOR, on human GC cells. PF-04979064 significantly inhibited the proliferation of human gastric adenocarcinoma AGS cells and the undifferentiated GC cell line HGC-27, promoting cell apoptosis. Combination treatment with PF-04979064 and the GC first-line clinical drug 5-FU showed synergistic effects, and PF-04979064 markedly increased the sensitivity of GC cells to chemotherapy drugs. Western blot results showed that PF-04979064 significantly inhibited the PI3K/AKT/mTOR signaling pathway in GC cells, whereas RNA seq results demonstrated substantial alterations in gene expression profiles upon treatment with PF-04979064. This study provides insight into the effects of PF-04979064, thereby establishing a solid foundation for its potential clinical application in the treatment of GC.
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Affiliation(s)
- Ziyuan Zhong
- School of Medical Laboratory, WeiFang Medical University, No.7166, Baotong West Street, Weifang, Shandong, 261053, China
| | - Tengkai Wang
- Cheeloo College of Medicine, Shandong University, No. 44 Wenhua West Road, Jinan, Shandong, 250012, China; Department of Gastroenterology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China
| | - Ruochen Zang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China
| | - Yufei Zang
- Cheeloo College of Medicine, Shandong University, No. 44 Wenhua West Road, Jinan, Shandong, 250012, China
| | - Yaoyao Feng
- Cheeloo College of Medicine, Shandong University, No. 44 Wenhua West Road, Jinan, Shandong, 250012, China
| | - Shujun Yan
- Department of Clinical Laboratory, Qilu Hospital of Shandong University (Qingdao), 758 Hefei Road, Qingdao, Shandong, 266035, China
| | - Congcong Geng
- Cheeloo College of Medicine, Shandong University, No. 44 Wenhua West Road, Jinan, Shandong, 250012, China
| | - Na Zhu
- Department of Clinical Laboratory, Qilu Hospital of Shandong University (Qingdao), 758 Hefei Road, Qingdao, Shandong, 266035, China
| | - Qian Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China; Department of Clinical Laboratory, Qilu Hospital of Shandong University (Qingdao), 758 Hefei Road, Qingdao, Shandong, 266035, China.
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2
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Green JR, Mahalingaiah PKS, Gopalakrishnan SM, Liguori MJ, Mittelstadt SW, Blomme EAG, Van Vleet TR. Off-target pharmacological activity at various kinases: Potential functional and pathological side effects. J Pharmacol Toxicol Methods 2023; 123:107468. [PMID: 37553032 DOI: 10.1016/j.vascn.2023.107468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/16/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
In drug discovery, during the lead optimization and candidate characterization stages, novel small molecules are frequently evaluated in a battery of in vitro pharmacology assays to identify potential unintended, off-target interactions with various receptors, transporters, ion channels, and enzymes, including kinases. Furthermore, these screening panels may also provide utility at later stages of development to provide a mechanistic understanding of unexpected safety findings. Here, we present a compendium of the most likely functional and pathological outcomes associated with interaction(s) to a panel of 95 kinases based on an extensive curation of the scientific literature. This panel of kinases was designed by AbbVie based on safety-related data extracted from the literature, as well as from over 20 years of institutional knowledge generated from discovery efforts. For each kinase, the scientific literature was reviewed using online databases and the most often reported functional and pathological effects were summarized. This work should serve as a practical guide for small molecule drug discovery scientists and clinical investigators to predict and/or interpret adverse effects related to pharmacological interactions with these kinases.
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Affiliation(s)
- Jonathon R Green
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States.
| | | | - Sujatha M Gopalakrishnan
- Drug Discovery Science and Technology, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Michael J Liguori
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Scott W Mittelstadt
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Eric A G Blomme
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Terry R Van Vleet
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
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3
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Chalfant V, Riveros C, Singh P, Shukla S, Balaji N, Balaji KC. Potential role for protein kinase D inhibitors in prostate cancer. J Mol Med (Berl) 2023. [PMID: 36843036 DOI: 10.1007/s00109-023-02298-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 02/01/2023] [Accepted: 02/10/2023] [Indexed: 02/28/2023]
Abstract
Protein kinase D (PrKD), a novel serine-threonine kinase, belongs to a family of calcium calmodulin kinases that consists of three isoforms: PrKD1, PrKD2, and PrKD3. The PrKD isoforms play a major role in pathologic processes such as cardiac hypertrophy and cancer progression. The charter member of the family, PrKD1, is the most extensively studied isoform. PrKD play a dual role as both a proto-oncogene and a tumor suppressor depending on the cellular context. The duplicity of PrKD can be highlighted in advanced prostate cancer (PCa) where expression of PrKD1 is suppressed whereas the expressions of PrKD2 and PrKD3 are upregulated to aid in cancer progression. As understanding of the PrKD signaling pathways has been better elucidated, interest has been garnered in the development of PrKD inhibitors. The broad-spectrum kinase inhibitor staurosporine acts as a potent PrKD inhibitor and is the most well-known; however, several other novel and more specific PrKD inhibitors have been developed over the last two decades. While there is tremendous potential for PrKD inhibitors to be used in a clinical setting, none has progressed beyond preclinical trials due to a variety of challenges. In this review, we focus on PrKD signaling in PCa and the potential role of PrKD inhibitors therein, and explore the possible clinical outcomes based on known function and expression of PrKD isoforms at different stages of PCa.
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Hajjo R, Sabbah DA, Abusara OH, Kharmah R, Bardaweel S. Targeting Human Proteins for Antiviral Drug Discovery and Repurposing Efforts: A Focus on Protein Kinases. Viruses 2023; 15. [PMID: 36851782 DOI: 10.3390/v15020568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/22/2023] Open
Abstract
Despite the great technological and medical advances in fighting viral diseases, new therapies for most of them are still lacking, and existing antivirals suffer from major limitations regarding drug resistance and a limited spectrum of activity. In fact, most approved antivirals are directly acting antiviral (DAA) drugs, which interfere with viral proteins and confer great selectivity towards their viral targets but suffer from resistance and limited spectrum. Nowadays, host-targeted antivirals (HTAs) are on the rise, in the drug discovery and development pipelines, in academia and in the pharmaceutical industry. These drugs target host proteins involved in the virus life cycle and are considered promising alternatives to DAAs due to their broader spectrum and lower potential for resistance. Herein, we discuss an important class of HTAs that modulate signal transduction pathways by targeting host kinases. Kinases are considered key enzymes that control virus-host interactions. We also provide a synopsis of the antiviral drug discovery and development pipeline detailing antiviral kinase targets, drug types, therapeutic classes for repurposed drugs, and top developing organizations. Furthermore, we detail the drug design and repurposing considerations, as well as the limitations and challenges, for kinase-targeted antivirals, including the choice of the binding sites, physicochemical properties, and drug combinations.
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5
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Marrone JI, Sepulchre JA, Ventura AC. A nested bistable module within a negative feedback loop ensures different types of oscillations in signaling systems. Sci Rep 2023; 13:529. [PMID: 36631477 DOI: 10.1038/s41598-022-27047-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023] Open
Abstract
In this article, we consider a double phosphorylation cycle, a ubiquitous signaling component, having the ability to display bistability, a behavior strongly related to the existence of positive feedback loops. If this component is connected to other signaling elements, it very likely undergoes some sort of protein-protein interaction. In several cases, these interactions result in a non-explicit negative feedback effect, leading to interlinked positive and negative feedbacks. This combination was studied in the literature as a way to generate relaxation-type oscillations. Here, we show that the two feedbacks together ensure two types of oscillations, the relaxation-type ones and a smoother type of oscillations functioning in a very narrow range of frequencies, in such a way that outside that range, the amplitude of the oscillations is severely compromised. Even more, we show that the two feedbacks are essential for both oscillatory types to emerge, and it is their hierarchy what determines the type of oscillation at work. We used bifurcation analyses and amplitude vs. frequency curves to characterize and classify the oscillations. We also applied the same ideas to another simple model, with the goal of generalizing what we learned from signaling models. The results obtained display the wealth of oscillatory dynamics that exists in a system with a bistable module nested within a negative feedback loop, showing how to transition between different types of oscillations and other dynamical behaviors such as excitability. Our work provides a framework for the study of other oscillatory systems based on bistable modules, from simple two-component models to more complex examples like the MAPK cascade and experimental cases like cell cycle oscillators.
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Torres-Quesada O, Strich S, Stefan E. Kinase perturbations redirect mitochondrial function in cancer. Bioenerg Commun 2022; 2022:17. [PMID: 37081928 PMCID: PMC7614455 DOI: 10.26124/bec:2022-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Protein kinases take the center stage in numerous signaling pathways by phosphorylating compartmentalized protein substrates for controlling cell proliferation, cell cycle and metabolism. Kinase dysfunctions have been linked to numerous human diseases such as cancer. This has led to the development of kinase inhibitors which aim to target oncogenic kinase activities. The specificity of the cancer blockers depends on the range of targeted kinases. Therefore, the question arises of how cell-type-specific off-target effects impair the specificities of cancer drugs. Blockade of kinase activities has been shown to converge on the energetic organelle, the mitochondria. In this review, we highlight examples of selected major kinases that impact mitochondrial signaling. Further, we discuss pharmacological strategies to target kinase activities linked to cancer progression and redirecting mitochondrial function. Finally, we propose that cell-based recordings of mitochondrial bioenergetic states might predict off-target or identify specific on-target effects of kinase inhibitors.
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Affiliation(s)
- Omar Torres-Quesada
- Tyrolean Cancer Research Institute, Innrain 66, 6020 Innsbruck, Austria
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
- Corresponding authors: ;
| | - Sophie Strich
- Tyrolean Cancer Research Institute, Innrain 66, 6020 Innsbruck, Austria
| | - Eduard Stefan
- Tyrolean Cancer Research Institute, Innrain 66, 6020 Innsbruck, Austria
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
- Corresponding authors: ;
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7
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Kochen MA, Andrews SS, Wiley HS, Feng S, Sauro HM. Dynamics and Sensitivity of Signaling Pathways. Curr Pathobiol Rep 2022; 10:11-22. [PMID: 36969954 PMCID: PMC10035447 DOI: 10.1007/s40139-022-00230-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Purpose of Review Signaling pathways serve to communicate information about extracellular conditions into the cell, to both the nucleus and cytoplasmic processes to control cell responses. Genetic mutations in signaling network components are frequently associated with cancer and can result in cells acquiring an ability to divide and grow uncontrollably. Because signaling pathways play such a significant role in cancer initiation and advancement, their constituent proteins are attractive therapeutic targets. In this review, we discuss how signaling pathway modeling can assist with identifying effective drugs for treating diseases, such as cancer. An achievement that would facilitate the use of such models is their ability to identify controlling biochemical parameters in signaling pathways, such as molecular abundances and chemical reaction rates, because this would help determine effective points of attack by therapeutics. Recent Findings We summarize the current state of understanding the sensitivity of phosphorylation cycles with and without sequestration. We also describe some basic properties of regulatory motifs including feedback and feedforward regulation. Summary Although much recent work has focused on understanding the dynamics and particularly the sensitivity of signaling networks in eukaryotic systems, there is still an urgent need to build more scalable models of signaling networks that can appropriately represent their complexity across different cell types and tumors.
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8
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Stephens M, Keane K, Roizes S, Liao S, Weid PYVD. Mincle-binding DNA aptamer demonstrates therapeutic potential in a model of inflammatory bowel disease. Molecular Therapy - Nucleic Acids 2022; 28:935-947. [PMID: 35782912 PMCID: PMC9207717 DOI: 10.1016/j.omtn.2022.05.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/12/2022] [Indexed: 10/25/2022]
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9
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Shah P, McGuigan CW, Cheng S, Vanpouille-Box C, Demaria S, Weiss RS, Lammerding J. ATM Modulates Nuclear Mechanics by Regulating Lamin A Levels. Front Cell Dev Biol 2022; 10:875132. [PMID: 35721517 PMCID: PMC9198445 DOI: 10.3389/fcell.2022.875132] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 05/13/2022] [Indexed: 12/18/2022] Open
Abstract
Ataxia-telangiectasia mutated (ATM) is one of the three main apical kinases at the crux of DNA damage response and repair in mammalian cells. ATM activates a cascade of downstream effector proteins to regulate DNA repair and cell cycle checkpoints in response to DNA double-strand breaks. While ATM is predominantly known for its role in DNA damage response and repair, new roles of ATM have recently begun to emerge, such as in regulating oxidative stress or metabolic pathways. Here, we report the surprising discovery that ATM inhibition and deletion lead to reduced expression of the nuclear envelope protein lamin A. Lamins are nuclear intermediate filaments that modulate nuclear shape, structure, and stiffness. Accordingly, inhibition or deletion of ATM resulted in increased nuclear deformability and enhanced cell migration through confined spaces, which requires substantial nuclear deformation. These findings point to a novel connection between ATM and lamin A and may have broad implications for cells with ATM mutations—as found in patients suffering from Ataxia Telangiectasia and many human cancers—which could lead to enhanced cell migration and increased metastatic potential.
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Affiliation(s)
- Pragya Shah
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States
| | - Connor W. McGuigan
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States
| | - Svea Cheng
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States
| | - Claire Vanpouille-Box
- Department of Radiation Oncology, Weill Cornell Medicine, New York City, NY, United States
| | - Sandra Demaria
- Department of Radiation Oncology, Weill Cornell Medicine, New York City, NY, United States
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, United States
| | - Robert S. Weiss
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States
| | - Jan Lammerding
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, United States
- *Correspondence: Jan Lammerding,
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10
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Nadeem A, Alam A, Toh E, Myint SL, Ur Rehman Z, Liu T, Bally M, Arnqvist A, Wang H, Zhu J, Persson K, Uhlin BE, Wai SN. Phosphatidic acid-mediated binding and mammalian cell internalization of the Vibrio cholerae cytotoxin MakA. PLoS Pathog 2021; 17:e1009414. [PMID: 33735319 DOI: 10.1371/journal.ppat.1009414] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/30/2021] [Accepted: 02/22/2021] [Indexed: 01/08/2023] Open
Abstract
Vibrio cholerae is a noninvasive intestinal pathogen extensively studied as the causative agent of the human disease cholera. Our recent work identified MakA as a potent virulence factor of V. cholerae in both Caenorhabditis elegans and zebrafish, prompting us to investigate the potential contribution of MakA to pathogenesis also in mammalian hosts. In this study, we demonstrate that the MakA protein could induce autophagy and cytotoxicity of target cells. In addition, we observed that phosphatidic acid (PA)-mediated MakA-binding to the host cell plasma membranes promoted macropinocytosis resulting in the formation of an endomembrane-rich aggregate and vacuolation in intoxicated cells that lead to induction of autophagy and dysfunction of intracellular organelles. Moreover, we functionally characterized the molecular basis of the MakA interaction with PA and identified that the N-terminal domain of MakA is required for its binding to PA and thereby for cell toxicity. Furthermore, we observed that the ΔmakA mutant outcompeted the wild-type V. cholerae strain A1552 in the adult mouse infection model. Based on the findings revealing mechanistic insights into the dynamic process of MakA-induced autophagy and cytotoxicity we discuss the potential role played by the MakA protein during late stages of cholera infection as an anti-colonization factor. Vibrio cholerae is the cause of cholera, an infectious disease causing watery diarrhea that can lead to fatal dehydration. The bacteria can readily adapt to different environments, such as from its natural aquatic habitats to the human digestive system. Recently, we reported a novel V. cholerae cytotoxin, MakA that functions as a potent virulence factor in C. elegans and zebrafish. Here we identified phosphatidic acid as a lipid target for MakA interaction with mammalian cells. This interaction promoted macropinocytosis resulting in the formation of an endomembrane-rich aggregate in intoxicated cells that ultimately lead to activation of autophagy. Importantly, data from bacterial colonization in a mouse infection model suggested that MakA might act as an anti-colonization factor of V. cholerae, presumably expressed during later stage(s) of infection. MakA might be explored as a new target for diagnostics and therapeutic developments against V. cholerae infections. Our findings will contribute to further understanding of the virulence, colonization and post-infection spread of V. cholerae.
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Peerzada M, Khan P, Khan NS, Avecilla F, Siddiqui SM, Hassan MI, Azam A. Design and Development of Small-Molecule Arylaldoxime/5-Nitroimidazole Hybrids as Potent Inhibitors of MARK4: A Promising Approach for Target-Based Cancer Therapy. ACS Omega 2020; 5:22759-22771. [PMID: 32954123 PMCID: PMC7495461 DOI: 10.1021/acsomega.0c01703] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/17/2020] [Indexed: 05/28/2023]
Abstract
Microtubule affinity-regulating kinase 4 (MARK4), a member of the serine/threonine kinase family, is an emerging therapeutic target in anticancer drug discovery paradigm due to its involvement in regulation of microtubule dynamics, cell cycle regulation, and cancer progression. Therefore, to identify the novel chemical architecture for the design and development of novel MARK4 inhibitors with concomitant radical scavenging property, a series of small-molecule arylaldoxime/5-nitroimidazole conjugates were designed and synthesized via multistep chemical reactions following the pharmacophoric hybridization approach. Compound 4h was identified as a promising MARK4 inhibitor with high selectivity toward MARK4 inhibition as compared to the panel of screened 30 kinases pertaining to the serine/threonine family, which was validated by molecular docking and fluorescence binding studies. The comprehensive cell-based examination divulged the promising apoptotic, antiproliferative, and antioxidant potential for the chemotype 4h. The compound 4h was endowed with the K a value of 3.6 × 103 M-1 for human serum albumin, which reflects its remarkable transportation and delivery properties to the target site via blood. The present study impedes that in the future, such compounds may stand as optimized pharmacological lead candidates in drug discovery for targeting cancer via MARK4 inhibition with a remarkable anticancer profile.
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Affiliation(s)
- Mudasir
Nabi Peerzada
- Medicinal
Chemistry Research Laboratory, Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Parvez Khan
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Nashrah Sharif Khan
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
- Department
of Biotechnology, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Fernando Avecilla
- Grupo
Xenomar, Centro de Investigacións Científicas Avanzadas
(CICA), Departamento de Química, Facultade de Ciencias, Universidade da Coruña, Campus A Coruña, 15071 A Coruña, Spain
| | - Shadab Miyan Siddiqui
- Medicinal
Chemistry Research Laboratory, Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Md. Imtaiyaz Hassan
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Amir Azam
- Medicinal
Chemistry Research Laboratory, Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
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12
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Thayer KM, Carcamo C. Homologs of the Tumor Suppressor Protein p53: A Bioinformatics Study for Drug Design. MOJ Proteom Bioinform 2020; 9:5-14. [PMID: 34532721 PMCID: PMC8442938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Sequence and structure of proteins related to the tumor suppressor protein p53 were studied from the perspective of gaining insight for the development of therapeutic drugs. Our study addresses two major issues encumber bringing novel drugs to market: side effects and artifacts from animal models. In the first phase of our study, we performed a genome-wide search to identify potentially similar proteins to p53 that may be susceptible to off target effects. In the second phase, we chose a selection of common model organisms that could potentially be available to undergraduate researchers in the university setting to assess which ones utilize p53 most similar to humans on the basis of sequence homology and structural similarity from predicted structures. Our results confirm the proteins in the humans significantly similar to p53 are known paralogs within the p53 family. In considering model organisms, murine p53 bore great similarity to human p53 in terms of both sequence and structure, but others performed similarly well. We discuss the findings against the background of other structural benchmarks and point out potential benefits and drawbacks of various alternatives for use in future drug design pilot studies.
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Affiliation(s)
- Kelly M Thayer
- Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
| | - Claudia Carcamo
- Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
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13
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López-Alonso I, Blázquez-Prieto J, Amado-Rodríguez L, González-López A, Astudillo A, Sánchez M, Huidobro C, López-Martínez C, Dos Santos CC, Albaiceta GM. Preventing loss of mechanosensation by the nuclear membranes of alveolar cells reduces lung injury in mice during mechanical ventilation. Sci Transl Med 2019; 10:10/456/eaam7598. [PMID: 30158154 DOI: 10.1126/scitranslmed.aam7598] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 08/30/2017] [Accepted: 01/25/2018] [Indexed: 01/08/2023]
Abstract
The nuclear membrane acts as a mechanosensor that drives cellular responses following changes in the extracellular environment. Mechanically ventilated lungs are exposed to an abnormally high mechanical load that may result in clinically relevant alveolar damage. We report that mechanical ventilation in mice increased the expression of Lamin-A, a major determinant of nuclear membrane stiffness, in alveolar epithelial cells. Lamin-A expression increased and nuclear membrane compliance decreased in human bronchial epithelial cells after a mechanical stretch stimulus and in a murine model of lung injury after positive-pressure ventilation. Reducing Lamin-A maturation by depletion of the protease-encoding gene Zmpste24 preserved alveolar nuclear membrane compliance after mechanical ventilation in mice. Ventilator-induced proapoptotic gene expression changes and lung injury were reduced in mice lacking Zmpste24 compared to wild-type control animals. Similarly, treatment with the human immunodeficiency virus protease inhibitors lopinavir and ritonavir reduced the accumulation of Lamin-A at nuclear membranes and preserved nuclear membrane compliance after mechanical ventilation, mimicking the protective phenotype of Zmpste24-/- animals. These results show that the pathophysiological response to lung mechanical stretch is sensed by the nuclear membranes of lung alveolar cells, and suggest that protease inhibitors might be effective in preventing ventilator-induced lung injury.
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Affiliation(s)
- Inés López-Alonso
- Área del Corazón, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain.,Departamento de Biología Funcional, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33005 Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain.,Centro de Investigación Biomédica En Red-Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Jorge Blázquez-Prieto
- Área del Corazón, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain.,Departamento de Biología Funcional, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33005 Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain.,Centro de Investigación Biomédica En Red-Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Laura Amado-Rodríguez
- Área del Corazón, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain.,Centro de Investigación Biomédica En Red-Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Adrián González-López
- Centro de Investigación Biomédica En Red-Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain.,Department of Anesthesiology and Operative Intensive Care Medicine, Charité Universitätsmedizin, 10117 Berlin, Germany
| | - Aurora Astudillo
- Servicio de Anatomía Patológica, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain.,Departamento de Cirugía y Especialidades Médicoquirúrgicas, Universidad de Oviedo, 33005 Oviedo, Spain
| | - Manuel Sánchez
- Área de Farmacología, Departamento de Medicina, Universidad de Oviedo, 33005 Oviedo, Spain
| | - Covadonga Huidobro
- Área del Corazón, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain.,Centro de Investigación Biomédica En Red-Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Cecilia López-Martínez
- Departamento de Biología Funcional, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33005 Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain
| | - Claudia C Dos Santos
- Interdepartmental Division of Critical Care, Keenan Research Centre of the Li Ka Shing Knowledge Institute of St. Michael's Hospital, University of Toronto, Toronto, Ontario M5B 1WB, Canada
| | - Guillermo M Albaiceta
- Área del Corazón, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain. .,Departamento de Biología Funcional, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33005 Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain.,Centro de Investigación Biomédica En Red-Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
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14
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Aljoundi AK, Agoni C, Olotu FA, Soliman ME. 'Piperazining' the catalytic gatekeepers: unraveling the pan-inhibition of SRC kinases; LYN, FYN and BLK by masitinib. Future Med Chem 2019; 11:2365-80. [PMID: 31516031 DOI: 10.4155/fmc-2018-0354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: Blocking oncogenic signaling of B-cell receptor (BCR) has been explored as a viable strategy in the treatment of diffuse large B-cell lymphoma. Masitinib is shown to multitarget LYN, FYN and BLK kinases that propagate BCR signals to downstream effectors. However, the molecular mechanisms of its selectivity and pan-inhibition remain elusive. Materials & methods: This study therefore employed molecular dynamics simulations coupled with advanced post-molecular dynamics simulation techniques to unravel the structural mechanisms that inform the reported multitargeting ability of masitinib. Results: Molecular dynamics simulations revealed initial selective targeting of catalytic residues (Asp334/Glu335 - LYN; Asp130/Asp148/Glu54 - FYN; Asp89 - BLK) by masitinib, with high-affinity interactions via its piperazine ring at the entrance of the ATP-binding pockets, before systematic access into the hydrophobic deep pocket grooves. Conclusion: Identification of these 'gatekeeper' residues could open up a novel paradigm of structure-based design of highly selective pan-inhibitors of BCR signaling in the treatment of diffuse large B-cell lymphoma.
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15
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Paul D, Radde N. The role of stochastic sequestration dynamics for intrinsic noise filtering in signaling network motifs. J Theor Biol 2018; 455:86-96. [PMID: 30017944 DOI: 10.1016/j.jtbi.2018.07.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/29/2018] [Accepted: 07/10/2018] [Indexed: 11/25/2022]
Abstract
The relation between design principles of signaling network motifs and their robustness against intrinsic noise still remains illusive. In this work we investigate the role of cascading for coping with intrinsic noise due to stochasticity in molecular reactions. We use stochastic approaches to quantify fluctuations in the terminal kinase of phosphorylation-dephosphorylation cascade motifs and demonstrate that cascading highly affects these fluctuations. We show that this purely stochastic effect can be explained by time-varying sequestration of upstream kinase molecules. In particular, we discuss conditions on time scales and parameter regimes which lead to a reduction of output fluctuations. Our results are put into biological context by adapting rate parameters of our modeling approach to biologically feasible ranges for general binding-unbinding and phosphorylation-dephosphorylation mechanisms. Overall, this study reveals a novel role of stochastic sequestration for dynamic noise filtering in signaling cascade motifs.
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Affiliation(s)
- Debdas Paul
- Institute for Systems Theory and Automatic Control, University of Stuttgart, Pfaffenwaldring 9, Stuttgart 70569, Germany.
| | - Nicole Radde
- Institute for Systems Theory and Automatic Control, University of Stuttgart, Pfaffenwaldring 9, Stuttgart 70569, Germany
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16
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Catozzi S, Sepulchre JA. A Discrete Dynamical System Approach to Pathway Activation Profiles of Signaling Cascades. Bull Math Biol 2017; 79:1691-735. [PMID: 28660544 DOI: 10.1007/s11538-017-0296-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 05/16/2017] [Indexed: 10/19/2022]
Abstract
In living organisms, cascades of covalent modification cycles are one of the major intracellular signaling mechanisms, allowing to transduce physical or chemical stimuli of the external world into variations of activated biochemical species within the cell. In this paper, we develop a novel method to study the stimulus-response of signaling cascades and overall the concept of pathway activation profile which is, for a given stimulus, the sequence of activated proteins at each tier of the cascade. Our approach is based on a correspondence that we establish between the stationary states of a cascade and pieces of orbits of a 2D discrete dynamical system. The study of its possible phase portraits in function of the biochemical parameters, and in particular of the contraction/expansion properties around the fixed points of this discrete map, as well as their bifurcations, yields a classification of the cascade tiers into three main types, whose biological impact within a signaling network is examined. In particular, our approach enables to discuss quantitatively the notion of cascade amplification/attenuation from this new perspective. The method allows also to study the interplay between forward and "retroactive" signaling, i.e., the upstream influence of an inhibiting drug bound to the last tier of the cascade.
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17
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Harada T, Yoshimura K, Yamashita O, Ueda K, Morikage N, Sawada Y, Hamano K. Focal Adhesion Kinase Promotes the Progression of Aortic Aneurysm by Modulating Macrophage Behavior. Arterioscler Thromb Vasc Biol 2016; 37:156-165. [PMID: 27856458 DOI: 10.1161/atvbaha.116.308542] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/31/2016] [Indexed: 01/18/2023]
Abstract
OBJECTIVE Abdominal aortic aneurysm (AAA) is a life-threatening vascular disease that is associated with persistent inflammation and extracellular matrix degradation. The molecular mechanisms underlying the macrophage-mediated progression of AAA remain largely unclear. APPROACH AND RESULTS We show that focal adhesion kinase (FAK) expression and activity are enhanced in macrophages that are recruited to AAA tissue. FAK potentiates tumor necrosis factor-α-induced secretion of matrix-degrading enzymes and chemokines by cultured macrophages. FAK also promotes macrophage chemotaxis. In mice, the administration of a FAK inhibitor that tempers local macrophage accumulation markedly suppresses the development and progression of chemically induced AAA. CONCLUSIONS FAK plays a key role in macrophage behavior, which underlies the chronic progression of AAA. These findings provide insights into AAA progression and identify FAK as a novel therapeutic target.
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Affiliation(s)
- Takasuke Harada
- From the Department of Surgery and Clinical Science, Yamaguchi University Graduate School of Medicine, Ube, Japan (T.H., K.Y., O.Y., K.U., N.M., K.H.); Graduate School of Health and Welfare, Yamaguchi Prefectural University, Japan (K.Y.); Department of Rehabilitation for the Movement Functions, Research Institute, National Rehabilitation Center for Persons with Disabilities, Tokorozawa, Japan (Y.S.)
| | - Koichi Yoshimura
- From the Department of Surgery and Clinical Science, Yamaguchi University Graduate School of Medicine, Ube, Japan (T.H., K.Y., O.Y., K.U., N.M., K.H.); Graduate School of Health and Welfare, Yamaguchi Prefectural University, Japan (K.Y.); Department of Rehabilitation for the Movement Functions, Research Institute, National Rehabilitation Center for Persons with Disabilities, Tokorozawa, Japan (Y.S.).
| | - Osamu Yamashita
- From the Department of Surgery and Clinical Science, Yamaguchi University Graduate School of Medicine, Ube, Japan (T.H., K.Y., O.Y., K.U., N.M., K.H.); Graduate School of Health and Welfare, Yamaguchi Prefectural University, Japan (K.Y.); Department of Rehabilitation for the Movement Functions, Research Institute, National Rehabilitation Center for Persons with Disabilities, Tokorozawa, Japan (Y.S.)
| | - Koshiro Ueda
- From the Department of Surgery and Clinical Science, Yamaguchi University Graduate School of Medicine, Ube, Japan (T.H., K.Y., O.Y., K.U., N.M., K.H.); Graduate School of Health and Welfare, Yamaguchi Prefectural University, Japan (K.Y.); Department of Rehabilitation for the Movement Functions, Research Institute, National Rehabilitation Center for Persons with Disabilities, Tokorozawa, Japan (Y.S.)
| | - Noriyasu Morikage
- From the Department of Surgery and Clinical Science, Yamaguchi University Graduate School of Medicine, Ube, Japan (T.H., K.Y., O.Y., K.U., N.M., K.H.); Graduate School of Health and Welfare, Yamaguchi Prefectural University, Japan (K.Y.); Department of Rehabilitation for the Movement Functions, Research Institute, National Rehabilitation Center for Persons with Disabilities, Tokorozawa, Japan (Y.S.)
| | - Yasuhiro Sawada
- From the Department of Surgery and Clinical Science, Yamaguchi University Graduate School of Medicine, Ube, Japan (T.H., K.Y., O.Y., K.U., N.M., K.H.); Graduate School of Health and Welfare, Yamaguchi Prefectural University, Japan (K.Y.); Department of Rehabilitation for the Movement Functions, Research Institute, National Rehabilitation Center for Persons with Disabilities, Tokorozawa, Japan (Y.S.)
| | - Kimikazu Hamano
- From the Department of Surgery and Clinical Science, Yamaguchi University Graduate School of Medicine, Ube, Japan (T.H., K.Y., O.Y., K.U., N.M., K.H.); Graduate School of Health and Welfare, Yamaguchi Prefectural University, Japan (K.Y.); Department of Rehabilitation for the Movement Functions, Research Institute, National Rehabilitation Center for Persons with Disabilities, Tokorozawa, Japan (Y.S.)
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18
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Catozzi S, Di-Bella JP, Ventura AC, Sepulchre JA. Signaling cascades transmit information downstream and upstream but unlikely simultaneously. BMC Syst Biol 2016; 10:84. [PMID: 27561377 PMCID: PMC5000522 DOI: 10.1186/s12918-016-0303-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/30/2016] [Indexed: 11/10/2022]
Abstract
Background Signal transduction is the process through which cells communicate with the external environment, interpret stimuli and respond to them. This mechanism is controlled by signaling cascades, which play the role of intracellular transmitter, being able to transmit biochemical information between cell membrane and nucleus. In theory as well as in practice, it has been shown that a perturbation can propagate upstream (and not only downstream) a cascade, by a mechanism known as retroactivity. This study aims to compare the conditions on biochemical parameters which favor one or the other direction of signaling in such a cascade. Results From a mathematical point of view, we show that the steady states of a cascade of arbitrary length n are described by an iterative map of second order, meaning that the cascade tiers are actually coupled three-by-three. We study the influence of the biochemical parameters in the control of the direction of transmission – upstream and/or downstream – along a signaling cascade. A numerical and statistical approach, based on the random scan of parameters describing a 3-tier signaling cascade, provides complementary findings to the analytical study. In particular, computing the likelihood of parameters with respect to various signaling regimes, we identify conditions on biochemical parameters which enhance a specific direction of propagation corresponding to forward or retro-signaling regimes. A compact graphical representation is designed to relay the gist of these conditions. Conclusions The values of biochemical parameters such as kinetic rates, Michaelis-Menten constants, total concentrations of kinases and of phosphatases, determine the propensity of a cascade to favor or impede downstream or upstream signal transmission. We found that generally there is an opposition between parameter sets favoring forward and retro-signaling regimes. Therefore, on one hand our study supports the idea that in most cases, retroactive effects can be neglected when a cascade which is efficient in forward signaling, is perturbed by an external ligand inhibiting the activation at some tier of the cascade. This result is relevant for therapeutic methodologies based on kinase inhibition. On the other hand, our study highlights a less-known part of the parameter space where, although the forward signaling is inefficient, the cascade can interestingly act as a retro-signaling device. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0303-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Simona Catozzi
- Université Côte d'Azur, CNRS, INLN, 1361 route des lucioles, Valbonne, 06560, France
| | - Juan Pablo Di-Bella
- IFIBYNE-UBA-CONICET and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires, C1428EHA, Argentina
| | - Alejandra C Ventura
- IFIBYNE-UBA-CONICET and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires, C1428EHA, Argentina
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19
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Gierut JJ, Wood LB, Lau KS, Lin YJ, Genetti C, Samatar AA, Lauffenburger DA, Haigis KM. Network-level effects of kinase inhibitors modulate TNF-α-induced apoptosis in the intestinal epithelium. Sci Signal 2015; 8:ra129. [PMID: 26671150 DOI: 10.1126/scisignal.aac7235] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Individual signaling pathways operate in the context of the broader signaling network. Thus, the response of a cell to signals from the environment is affected by the state of the signaling network, such as the clinically relevant example of whether some components in the network are inhibited. The cytokine tumor necrosis factor-α (TNF-α) promotes opposing cellular behaviors under different conditions; the outcome is influenced by the state of the network. For example, in the mouse intestinal epithelium, inhibition of the mitogen-activated protein kinase (MAPK) kinase MEK alters the timing of TNF-α-induced apoptosis. We investigated whether MAPK signaling directly influences TNF-α-induced apoptosis or whether network-level effects secondary to inhibition of the MAPK pathway alter the cellular response. We found that inhibitors of the MAPK kinase kinase Raf, MEK, or extracellular signal-regulated kinase (ERK) exerted distinct effects on the timing and magnitude of TNF-α-induced apoptosis in the mouse intestine. Furthermore, even different MEK inhibitors exerted distinct effects; one, CH5126766, potentiated TNF-α-induced apoptosis, and the others reduced cell death. Computational modeling and experimental perturbation identified the kinase Akt as the primary signaling node that enhanced apoptosis in the context of TNF-α signaling in the presence of CH5126766. Our work emphasizes the importance of integrated network signaling in specifying cellular behavior in response to experimental or therapeutic manipulation. More broadly, this study highlighted the importance of considering the network-level effects of pathway inhibitors and showed the distinct effects of inhibitors that share the same target.
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Affiliation(s)
- Jessica J Gierut
- Cancer Research Institute, Beth Israel Deaconess Cancer Center and Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Levi B Wood
- Cancer Research Institute, Beth Israel Deaconess Cancer Center and Department of Medicine, Harvard Medical School, Boston, MA 02215, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ken S Lau
- Department of Chemical and Physical Biology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.,Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Yi-Jang Lin
- Cancer Research Institute, Beth Israel Deaconess Cancer Center and Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Casie Genetti
- Cancer Research Institute, Beth Israel Deaconess Cancer Center and Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | | | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kevin M Haigis
- Cancer Research Institute, Beth Israel Deaconess Cancer Center and Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
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20
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Geman D, Ochs M, Price ND, Tomasetti C, Younes L. An argument for mechanism-based statistical inference in cancer. Hum Genet 2014; 134:479-95. [PMID: 25381197 DOI: 10.1007/s00439-014-1501-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 10/14/2014] [Indexed: 01/07/2023]
Abstract
Cancer is perhaps the prototypical systems disease, and as such has been the focus of extensive study in quantitative systems biology. However, translating these programs into personalized clinical care remains elusive and incomplete. In this perspective, we argue that realizing this agenda—in particular, predicting disease phenotypes, progression and treatment response for individuals—requires going well beyond standard computational and bioinformatics tools and algorithms. It entails designing global mathematical models over network-scale configurations of genomic states and molecular concentrations, and learning the model parameters from limited available samples of high-dimensional and integrative omics data. As such, any plausible design should accommodate: biological mechanism, necessary for both feasible learning and interpretable decision making; stochasticity, to deal with uncertainty and observed variation at many scales; and a capacity for statistical inference at the patient level. This program, which requires a close, sustained collaboration between mathematicians and biologists, is illustrated in several contexts, including learning biomarkers, metabolism, cell signaling, network inference and tumorigenesis.
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Affiliation(s)
- Donald Geman
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, 21210, USA,
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21
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Wynn ML, Consul N, Merajver SD, Schnell S. Inferring the Effects of Honokiol on the Notch Signaling Pathway in SW480 Colon Cancer Cells. Cancer Inform 2014; 13:1-12. [PMID: 25392689 PMCID: PMC4218690 DOI: 10.4137/cin.s14060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 08/27/2014] [Accepted: 08/27/2014] [Indexed: 12/13/2022] Open
Abstract
In a tumor cell, the development of acquired therapeutic resistance and the ability to survive in extracellular environments that differ from the primary site are the result of molecular adaptations in potentially highly plastic molecular networks. The accurate prediction of intracellular networks in a tumor remains a difficult problem in cancer informatics. In order to make truly rational patient-driven therapeutic decisions, it will be critical to develop methodologies that can accurately infer the molecular circuitry in the cells of a specific tumor. Despite enormous heterogeneity, cellular networks elicit deterministic digital-like responses. We discuss the use and limitations of methodologies that model molecular networks in cancer cells as a digital circuit. We also develop a network model of Notch signaling in colon cancer using a novel reverse engineering logic-based method and published western blot data to elucidate the interactions likely present in the circuits of the SW480 colon cancer cell line. Within this framework, we make predictions related to the role that honokiol may be playing as an anti-cancer drug.
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Affiliation(s)
- Michelle L Wynn
- Department of Internal Medicine, Division of Hematology and Oncology and Comprehensive Cancer Center, University of Michigan, Medical School, Ann Arbor, MI, USA. ; Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA. ; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA. ; Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nikita Consul
- Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Sofia D Merajver
- Department of Internal Medicine, Division of Hematology and Oncology and Comprehensive Cancer Center, University of Michigan, Medical School, Ann Arbor, MI, USA
| | - Santiago Schnell
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA. ; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA. ; Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, MI, USA
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22
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Cheow LF, Sarkar A, Kolitz S, Lauffenburger D, Han J. Detecting kinase activities from single cell lysate using concentration-enhanced mobility shift assay. Anal Chem 2014; 86:7455-62. [PMID: 25025773 PMCID: PMC4144746 DOI: 10.1021/ac502185v] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Electrokinetic preconcentration coupled with mobility shift assays can give rise to very high detection sensitivities. We describe a microfluidic device that utilizes this principle to detect cellular kinase activities by simultaneously concentrating and separating substrate peptides with different phosphorylation states. This platform is capable of reliably measuring kinase activities of single adherent cells cultured in nanoliter volume microwells. We also describe a novel method utilizing spacer peptides that significantly increase separation resolution while maintaining high concentration factors in this device. Thus, multiplexed kinase measurements can be implemented with single cell sensitivity. Multiple kinase activity profiling from single cell lysate could potentially allow us to study heterogeneous activation of signaling pathways that can lead to multiple cell fates.
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Affiliation(s)
- Lih Feng Cheow
- Department of Electrical Engineering and Computer Science and ‡Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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23
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Wagner JP, Wolf-Yadlin A, Sevecka M, Grenier JK, Root DE, Lauffenburger DA, MacBeath G. Receptor tyrosine kinases fall into distinct classes based on their inferred signaling networks. Sci Signal 2013; 6:ra58. [PMID: 23861540 DOI: 10.1126/scisignal.2003994] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Although many anticancer drugs that target receptor tyrosine kinases (RTKs) provide clinical benefit, their long-term use is limited by resistance that is often attributed to increased abundance or activation of another RTK that compensates for the inhibited receptor. To uncover common and unique features in the signaling networks of RTKs, we measured time-dependent signaling in six isogenic cell lines, each expressing a different RTK as downstream proteins were systematically perturbed by RNA interference. Network models inferred from the data revealed a conserved set of signaling pathways and RTK-specific features that grouped the RTKs into three distinct classes: (i) an EGFR/FGFR1/c-Met class constituting epidermal growth factor receptor, fibroblast growth factor receptor 1, and the hepatocyte growth factor receptor c-Met; (ii) an IGF-1R/NTRK2 class constituting insulin-like growth factor 1 receptor and neurotrophic tyrosine receptor kinase 2; and (iii) a PDGFRβ class constituting platelet-derived growth factor receptor β. Analysis of cancer cell line data showed that many RTKs of the same class were coexpressed and that increased abundance of an RTK or its cognate ligand frequently correlated with resistance to a drug targeting another RTK of the same class. In contrast, abundance of an RTK or ligand of one class generally did not affect sensitivity to a drug targeting an RTK of a different class. Thus, classifying RTKs by their inferred networks and then therapeutically targeting multiple receptors within a class may delay or prevent the onset of resistance.
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Affiliation(s)
- Joel P Wagner
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Alejandro Wolf-Yadlin
- Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Mark Sevecka
- Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Jennifer K Grenier
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Gavin MacBeath
- Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.,Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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24
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Wynn ML, Consul N, Merajver SD, Schnell S. Logic-based models in systems biology: a predictive and parameter-free network analysis method. Integr Biol (Camb) 2013; 4:1323-37. [PMID: 23072820 DOI: 10.1039/c2ib20193c] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Highly complex molecular networks, which play fundamental roles in almost all cellular processes, are known to be dysregulated in a number of diseases, most notably in cancer. As a consequence, there is a critical need to develop practical methodologies for constructing and analysing molecular networks at a systems level. Mathematical models built with continuous differential equations are an ideal methodology because they can provide a detailed picture of a network's dynamics. To be predictive, however, differential equation models require that numerous parameters be known a priori and this information is almost never available. An alternative dynamical approach is the use of discrete logic-based models that can provide a good approximation of the qualitative behaviour of a biochemical system without the burden of a large parameter space. Despite their advantages, there remains significant resistance to the use of logic-based models in biology. Here, we address some common concerns and provide a brief tutorial on the use of logic-based models, which we motivate with biological examples.
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Affiliation(s)
- Michelle L Wynn
- Center for Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.
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25
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Sepulchre JA, Ventura AC. Intrinsic feedbacks in MAPK signaling cascades lead to bistability and oscillations. Acta Biotheor 2013; 61:59-78. [PMID: 23400325 DOI: 10.1007/s10441-013-9177-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 01/22/2013] [Indexed: 10/27/2022]
Abstract
Previous studies have demonstrated that double phosphorylation of a protein can lead to bistability if some conditions are fulfilled. It was also shown that the signaling behavior of a covalent modification cycle can be quantitatively and, more importantly, qualitatively modified when this cycle is coupled to a signaling pathway as opposed to being isolated. This property was named retroactivity. These two results are studied together in this paper showing the existence of interesting phenomena--oscillations and bistability--in signaling cascades possessing at least one stage with a double-phosphorylation cycle as in MAPK cascades.
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26
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Abstract
The current approach to treatment in oncology is to replace the generally cytotoxic chemotherapies with pharmaceutical treatment which inactivates specific molecular targets associated with cancer development and progression. The goal is to limit cellular damage to pathways perceived to be directly responsible for the malignancy. Its underlying assumptions are twofold: (1) that individual pathways are the cause of malignancy; and (2) that the treatment objective should be destruction-either of the tumor or the dysfunctional pathway. However, the extent to which data actually support these assumptions has not been directly addressed. Accumulating evidence suggests that systemic dysfunction precedes the disruption of specific genetic/molecular pathways in most adult cancers and that targeted treatments such as kinase inhibitors may successfully treat one pathway while generating unintended changes to other, non-targeted pathways. This article discusses (1) the systemic basis of malignancy; (2) better profiling of pre-cancerous biomarkers associated with elevated risk so that preventive lifestyle modifications can be instituted early to revert high-risk epigenetic changes before tumors develop; (3) a treatment emphasis in early stage tumors that would target the restoration of systemic balance by strengthening the body's innate defense mechanisms; and (4) establishing better quantitative models of systems to capture adequate complexity for predictability at all stages of tumor progression.
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Affiliation(s)
- Sarah S. Knox
- West Virginia University School of Public Health, Mary Babb Randolph Cancer Center, West Virginia University School of Medicine
| | - Michael F. Ochs
- Division of Oncology Biostatistics and Bioinformatics, Departments of Oncology and Health Science Informatics, Johns Hopkins University
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Ochs MF. Issues in Omics Data Integration for Gene Set Analysis and Aberrant Pathway Identification. Drug Dev Res 2012. [DOI: 10.1002/ddr.21046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Michael F. Ochs
- Department of Oncology; Johns Hopkins University; Baltimore; MD; 21218; USA
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Abstract
In biochemical signaling pathways without explicit feedback connections, the core signal transduction is usually described as a one-way communication, going from upstream to downstream in a feedforward chain or network of covalent modification cycles. In this paper we explore the possibility of a new type of signaling called retroactive signaling, offered by the recently demonstrated property of retroactivity in signaling cascades. The possibility of retroactive signaling is analysed in the simplest case of the stationary states of a bicyclic cascade of signaling cycles. In this case, we work out the conditions for which variables of the upstream cycle are affected by a change of the total amount of protein in the downstream cycle, or by a variation of the phosphatase deactivating the same protein. Particularly, we predict the characteristic ranges of the downstream protein, or of the downstream phosphatase, for which a retroactive effect can be observed on the upstream cycle variables. Next, we extend the possibility of retroactive signaling in short but nonlinear signaling pathways involving a few covalent modification cycles.
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Kannan Y, Wilson MS. TEC and MAPK Kinase Signalling Pathways in T helper (T H) cell Development, T H2 Differentiation and Allergic Asthma. J Clin Cell Immunol 2012; Suppl 12:11. [PMID: 24116341 PMCID: PMC3792371 DOI: 10.4172/2155-9899.s12-011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Significant advances in our understanding of the signalling events during T cell development and differentiation have been made in the past few decades. It is clear that ligation of the T cell receptor (TCR) triggers a series of proximal signalling cascades regulated by an array of protein kinases. These orchestrated and highly regulated series of events, with differential requirements of particular kinases, highlight the disparities between αβ+CD4+ T cells. Throughout this review we summarise both new and old studies, highlighting the role of Tec and MAPK in T cell development and differentiation with particular focus on T helper 2 (TH2) cells. Finally, as the allergy epidemic continues, we feature the role played by TH2 cells in the development of allergy and provide a brief update on promising kinase inhibitors that have been tested in vitro, in pre-clinical disease models in vivo and into clinical studies.
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Affiliation(s)
- Yashaswini Kannan
- Division of Molecular Immunology, National Institute for Medical Research, MRC, London, NW7 1AA, UK
| | - Mark S. Wilson
- Division of Molecular Immunology, National Institute for Medical Research, MRC, London, NW7 1AA, UK
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