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McPherson KS, Korzhnev DM. Targeting protein-protein interactions in the DNA damage response pathways for cancer chemotherapy. RSC Chem Biol 2021; 2:1167-1195. [PMID: 34458830 PMCID: PMC8342002 DOI: 10.1039/d1cb00101a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/20/2021] [Indexed: 12/11/2022] Open
Abstract
Cellular DNA damage response (DDR) is an extensive signaling network that orchestrates DNA damage recognition, repair and avoidance, cell cycle progression and cell death. DDR alteration is a hallmark of cancer, with the deficiency in one DDR capability often compensated by a dependency on alternative pathways endowing cancer cells with survival and growth advantage. Targeting these DDR pathways has provided multiple opportunities for the development of cancer therapies. Traditional drug discovery has mainly focused on catalytic inhibitors that block enzyme active sites, which limits the number of potential drug targets within the DDR pathways. This review article describes the emerging approach to the development of cancer therapeutics targeting essential protein-protein interactions (PPIs) in the DDR network. The overall strategy for the structure-based design of small molecule PPI inhibitors is discussed, followed by an overview of the major DNA damage sensing, DNA repair, and DNA damage tolerance pathways with a specific focus on PPI targets for anti-cancer drug design. The existing small molecule inhibitors of DDR PPIs are summarized that selectively kill cancer cells and/or sensitize cancers to front-line genotoxic therapies, and a range of new PPI targets are proposed that may lead to the development of novel chemotherapeutics.
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Affiliation(s)
- Kerry Silva McPherson
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center Farmington CT 06030 USA +1 860 679 3408 +1 860 679 2849
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center Farmington CT 06030 USA +1 860 679 3408 +1 860 679 2849
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2
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Saydmohammed M, Vollmer LL, Onuoha EO, Maskrey TS, Gibson G, Watkins SC, Wipf P, Vogt A, Tsang M. A High-Content Screen Reveals New Small-Molecule Enhancers of Ras/Mapk Signaling as Probes for Zebrafish Heart Development. Molecules 2018; 23:molecules23071691. [PMID: 29997348 PMCID: PMC6099644 DOI: 10.3390/molecules23071691] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/09/2018] [Accepted: 07/09/2018] [Indexed: 12/11/2022] Open
Abstract
Zebrafish is the preferred vertebrate model for high throughput chemical screens to discover modulators of complex biological pathways. We adapted a transgenic zebrafish line, Tg(dusp6:EGFP), which reports on fibroblast growth factor (Fgf)/Ras/Mapk activity, into a quantitative, high-content chemical screen to identify novel Fgf hyperactivators as chemical probes for zebrafish heart development and regeneration. We screened 10,000 compounds from the TimTec ActiProbe library, and identified several structurally distinct classes of molecules that enhanced Fgf/Ras/Mapk signaling. We chose three agents—ST020101, ST011282, and ST006994—for confirmatory and functional studies based on potency, repeatability with repurchased material, favorable whole organism toxicity, and evidence of structure–activity relationships. Functional follow-up assays confirmed that all three compounds induced the expression of Fgf target genes during zebrafish embryonic development. Moreover, these compounds increased cardiac progenitor populations by effecting a fate change from endothelial to cardiac progenitors that translated into increased numbers of cardiomyocytes. Interestingly, ST006994 augmented Fgf/Ras/Mapk signaling without increasing Erk phosphorylation, suggesting a molecular mechanism of action downstream of Erk. We posit that the ST006994 pharmacophore could become a unique chemical probe to uncover novel mechanisms of Fgf signaling during heart development and regeneration downstream of the Mapk signaling node.
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Affiliation(s)
- Manush Saydmohammed
- Department of Developmental Biology, University of Pittsburgh, BST3, 3501 5th Avenue, Pittsburgh, PA 15213, USA.
| | - Laura L Vollmer
- The University of Pittsburgh Drug Discovery Institute, 200 Lothrop Street, Pittsburgh, PA 15260, USA.
| | - Ezenwa O Onuoha
- Department of Developmental Biology, University of Pittsburgh, BST3, 3501 5th Avenue, Pittsburgh, PA 15213, USA.
| | - Taber S Maskrey
- Department of Chemistry, 219 University Drive, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Gregory Gibson
- Department of Cell Biology, University of Pittsburgh, 3500 Terrace Street, Pittsburgh, PA 15213, USA.
| | - Simon C Watkins
- Department of Cell Biology, University of Pittsburgh, 3500 Terrace Street, Pittsburgh, PA 15213, USA.
| | - Peter Wipf
- Department of Chemistry, 219 University Drive, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Andreas Vogt
- The University of Pittsburgh Drug Discovery Institute, 200 Lothrop Street, Pittsburgh, PA 15260, USA.
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA.
| | - Michael Tsang
- Department of Developmental Biology, University of Pittsburgh, BST3, 3501 5th Avenue, Pittsburgh, PA 15213, USA.
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3
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Kamal A, Nekkanti S, Shankaraiah N, Sathish M. Future of Drug Discovery. DRUG RESISTANCE IN BACTERIA, FUNGI, MALARIA, AND CANCER 2017:609-629. [DOI: 10.1007/978-3-319-48683-3_27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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Fang J, Pang X, Yan R, Lian W, Li C, Wang Q, Liu AL, Du GH. Discovery of neuroprotective compounds by machine learning approaches. RSC Adv 2016. [DOI: 10.1039/c5ra23035g] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The classification models were constructed to discover neuroprotective compounds against glutamate or H2O2-induced neurotoxicity through machine learning approaches.
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Affiliation(s)
- Jiansong Fang
- Institute of Materia Medica
- Chinese Academy of Medical Sciences and Peking Union Medical College
- Beijing 100050
- PR China
- Institute of Clinical Pharmacology
| | - Xiaocong Pang
- Institute of Materia Medica
- Chinese Academy of Medical Sciences and Peking Union Medical College
- Beijing 100050
- PR China
| | - Rong Yan
- Institute of Materia Medica
- Chinese Academy of Medical Sciences and Peking Union Medical College
- Beijing 100050
- PR China
| | - Wenwen Lian
- Institute of Materia Medica
- Chinese Academy of Medical Sciences and Peking Union Medical College
- Beijing 100050
- PR China
| | - Chao Li
- Institute of Materia Medica
- Chinese Academy of Medical Sciences and Peking Union Medical College
- Beijing 100050
- PR China
| | - Qi Wang
- Institute of Clinical Pharmacology
- Guangzhou University of Traditional Chinese Medicine
- Guangzhou 510006
- China
| | - Ai-Lin Liu
- Institute of Materia Medica
- Chinese Academy of Medical Sciences and Peking Union Medical College
- Beijing 100050
- PR China
- Beijing Key Laboratory of Drug Target and Screening Research
| | - Guan-Hua Du
- Institute of Materia Medica
- Chinese Academy of Medical Sciences and Peking Union Medical College
- Beijing 100050
- PR China
- Beijing Key Laboratory of Drug Target and Screening Research
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5
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Korotchenko VN, Saydmohammed M, Vollmer LL, Bakan A, Sheetz K, Debiec KT, Greene KA, Agliori CS, Bahar I, Day BW, Vogt A, Tsang M. In vivo structure-activity relationship studies support allosteric targeting of a dual specificity phosphatase. Chembiochem 2014; 15:1436-45. [PMID: 24909879 DOI: 10.1002/cbic.201402000] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Indexed: 11/06/2022]
Abstract
Dual specificity phosphatase 6 (DUSP6) functions as a feedback attenuator of fibroblast growth factor signaling during development. In vitro high throughput chemical screening attempts to discover DUSP6 inhibitors have yielded limited success. However, in vivo whole-organism screens of zebrafish identified compound 1 (BCI) as an allosteric inhibitor of DUSP6. Here we designed and synthesized a panel of analogues to define the structure-activity relationship (SAR) of DUSP6 inhibition. In vivo high-content analysis in transgenic zebrafish, coupled with cell-based chemical complementation assays, identified structural features of the pharmacophore of 1 that were essential for biological activity. In vitro assays of DUSP hyperactivation corroborated the results from in vivo and cellular SAR. The results reinforce the notion that DUSPs are druggable through allosteric mechanisms and illustrate the utility of zebrafish as a model organism for in vivo SAR analyses.
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Affiliation(s)
- Vasiliy N Korotchenko
- Department of Pharmaceutical Sciences, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15213 (USA); Present address: Walter Reed Army Institute of Research, 503 Forney Drive, Silver Spring, MD 20910 (USA)
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Zheng W, Thorne N, McKew JC. Phenotypic screens as a renewed approach for drug discovery. Drug Discov Today 2013; 18:1067-73. [PMID: 23850704 DOI: 10.1016/j.drudis.2013.07.001] [Citation(s) in RCA: 281] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 06/10/2013] [Accepted: 07/02/2013] [Indexed: 12/12/2022]
Abstract
The significant reduction in the number of newly approved drugs in the past decade has been partially attributed to failures in discovery and validation of new targets. Evaluation of recently approved new drugs has revealed that the number of approved drugs discovered through phenotypic screens, an original drug screening paradigm, has exceeded those discovered through the molecular target-based approach. Phenotypic screening is thus gaining new momentum in drug discovery with the hope that this approach may revitalize drug discovery and improve the success rate of drug approval through the discovery of viable lead compounds and identification of novel drug targets.
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Affiliation(s)
- Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA.
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Molina G, Vogt A, Bakan A, Dai W, Queiroz de Oliveira P, Znosko W, Smithgall TE, Bahar I, Lazo JS, Day BW, Tsang M. Zebrafish chemical screening reveals an inhibitor of Dusp6 that expands cardiac cell lineages. Nat Chem Biol 2009; 5:680-7. [PMID: 19578332 PMCID: PMC2771339 DOI: 10.1038/nchembio.190] [Citation(s) in RCA: 186] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Accepted: 04/30/2009] [Indexed: 11/09/2022]
Abstract
The dual specificity phosphatase 6 (Dusp6) functions as a feedback regulator of fibroblast growth factor (FGF) signaling to limit the activity of extracellular signal regulated kinase (ERK) 1 and 2. We have identified a small molecule inhibitor of Dusp6, (E)-2-benzylidene-3-(cyclohexylamino)-2,3-dihydro-1H-inden-1-one (BCI), using a transgenic zebrafish chemical screen. BCI treatment blocked Dusp6 activity and enhanced FGF target gene expression in zebrafish embryos. Docking simulations predicted an allosteric binding site for BCI within the phosphatase domain. In vitro studies supported a model that BCI inhibits Dusp6 catalytic activation by ERK2 substrate binding. A temporal role for Dusp6 in restricting cardiac progenitors and controlling heart organ size was uncovered with BCI treatment at varying developmental stages. This study highlights the power of in vivo zebrafish chemical screens to identify novel compounds targeting Dusp6, a component of the FGF signaling pathway that has eluded traditional high-throughput in vitro screens.
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Affiliation(s)
- Gabriela Molina
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Abraham SM, Clark AR. Dual-specificity phosphatase 1: a critical regulator of innate immune responses. Biochem Soc Trans 2006; 34:1018-23. [PMID: 17073741 DOI: 10.1042/bst0341018] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Innate immune responses are critically dependent on MAPK (mitogen-activated protein kinase) signalling pathways, in particular JNK (c-Jun N-terminal kinase) and p38 MAPK. Both of these kinases are negatively regulated via their dephosphorylation by DUSP1 (dual-specificity phosphatase 1). Several pro- and anti-inflammatory stimuli converge to regulate the DUSP1 gene and to modulate the time course of its expression. In turn, the pattern of expression of DUSP1 dictates the kinetics of activation of JNK and p38 MAPK, and this influences the expression of several mediators of innate immunity. DUSP1 is therefore a central regulator of innate immunity, and its expression can profoundly affect the outcome of inflammatory challenges. We discuss possible implications for immune-mediated inflammatory diseases and their treatment.
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Affiliation(s)
- S M Abraham
- Kennedy Institute of Rheumatology Division, Imperial College London, 1 Aspenlea Road, Hammersmith, London W6 8LH, UK
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