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Manen-Freixa L, Antolin AA. Polypharmacology prediction: the long road toward comprehensively anticipating small-molecule selectivity to de-risk drug discovery. Expert Opin Drug Discov 2024:1-27. [PMID: 39004919 DOI: 10.1080/17460441.2024.2376643] [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: 03/15/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024]
Abstract
INTRODUCTION Small molecules often bind to multiple targets, a behavior termed polypharmacology. Anticipating polypharmacology is essential for drug discovery since unknown off-targets can modulate safety and efficacy - profoundly affecting drug discovery success. Unfortunately, experimental methods to assess selectivity present significant limitations and drugs still fail in the clinic due to unanticipated off-targets. Computational methods are a cost-effective, complementary approach to predict polypharmacology. AREAS COVERED This review aims to provide a comprehensive overview of the state of polypharmacology prediction and discuss its strengths and limitations, covering both classical cheminformatics methods and bioinformatic approaches. The authors review available data sources, paying close attention to their different coverage. The authors then discuss major algorithms grouped by the types of data that they exploit using selected examples. EXPERT OPINION Polypharmacology prediction has made impressive progress over the last decades and contributed to identify many off-targets. However, data incompleteness currently limits most approaches to comprehensively predict selectivity. Moreover, our limited agreement on model assessment challenges the identification of the best algorithms - which at present show modest performance in prospective real-world applications. Despite these limitations, the exponential increase of multidisciplinary Big Data and AI hold much potential to better polypharmacology prediction and de-risk drug discovery.
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Affiliation(s)
- Leticia Manen-Freixa
- Oncobell Division, Bellvitge Biomedical Research Institute (IDIBELL) and ProCURE Department, Catalan Institute of Oncology (ICO), Barcelona, Spain
| | - Albert A Antolin
- Oncobell Division, Bellvitge Biomedical Research Institute (IDIBELL) and ProCURE Department, Catalan Institute of Oncology (ICO), Barcelona, Spain
- Center for Cancer Drug Discovery, The Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
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Iglesias P, Seoane M, Golán-Cancela I, Fraga M, Arce VM, Costoya JA. A New Opportunity for "Old" Molecules: Targeting PARP1 Activity through a Non-Enzymatic Mechanism. Int J Mol Sci 2023; 24:ijms24108849. [PMID: 37240195 DOI: 10.3390/ijms24108849] [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: 04/17/2023] [Revised: 05/10/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
In recent years, new therapies have been developed based on molecules that target molecular mechanisms involved in both the initiation and maintenance of the oncogenic process. Among these molecules are the poly(ADP-ribose) polymerase 1 (PARP1) inhibitors. PARP1 has emerged as a target with great therapeutic potential for some tumor types, drawing attention to this enzyme and resulting in many small molecule inhibitors of its enzymatic activity. Therefore, many PARP inhibitors are currently in clinical trials for the treatment of homologous recombination (HR)-deficient tumors, BRCA-related cancers, taking advantage of synthetic lethality. In addition, several novel cellular functions unrelated to its role in DNA repair have been described, including post-translational modification of transcription factors, or acting through protein-protein interactions as a co-activator or co-repressor of transcription. Previously, we reported that this enzyme may play a key role as a transcriptional co-activator of an important component of cell cycle regulation, the transcription factor E2F1. Here, we show that PARP inhibitors, which interfere with its activity in cell cycle regulation, perform this without affecting its enzymatic function.
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Affiliation(s)
- Pablo Iglesias
- Molecular Oncology Laboratory MOL, Departamento de Fisioloxía, Centro Singular de Investigación en Medicina Molecular e Enfermidades Crónicas (CiMUS), Facultade de Medicina, Universidade de Santiago de Compostela and Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), 15782 Santiago de Compostela, Spain
| | - Marcos Seoane
- Molecular Oncology Laboratory MOL, Departamento de Fisioloxía, Centro Singular de Investigación en Medicina Molecular e Enfermidades Crónicas (CiMUS), Facultade de Medicina, Universidade de Santiago de Compostela and Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), 15782 Santiago de Compostela, Spain
| | - Irene Golán-Cancela
- Molecular Oncology Laboratory MOL, Departamento de Fisioloxía, Centro Singular de Investigación en Medicina Molecular e Enfermidades Crónicas (CiMUS), Facultade de Medicina, Universidade de Santiago de Compostela and Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), 15782 Santiago de Compostela, Spain
| | - Máximo Fraga
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Universidade de Santiago de Compostela and Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), 15782 Santiago de Compostela, Spain
| | - Victor M Arce
- Molecular Oncology Laboratory MOL, Departamento de Fisioloxía, Centro Singular de Investigación en Medicina Molecular e Enfermidades Crónicas (CiMUS), Facultade de Medicina, Universidade de Santiago de Compostela and Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), 15782 Santiago de Compostela, Spain
| | - Jose A Costoya
- Molecular Oncology Laboratory MOL, Departamento de Fisioloxía, Centro Singular de Investigación en Medicina Molecular e Enfermidades Crónicas (CiMUS), Facultade de Medicina, Universidade de Santiago de Compostela and Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), 15782 Santiago de Compostela, Spain
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Cohen-Armon M. Exclusive modifications of NuMA in malignant epithelial cells: A potential therapeutic mechanism. Drug Discov Today 2022; 27:1205-1209. [PMID: 35143964 DOI: 10.1016/j.drudis.2022.02.002] [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: 09/02/2021] [Revised: 12/13/2021] [Accepted: 02/03/2022] [Indexed: 11/03/2022]
Abstract
NuMA (nuclear mitotic apparatus) protein is indispensable in the mitosis of human proliferating cells, both malignant and benign. The progression of mitosis requires stable spindles, which depend on the bipolar clustering of NuMA within the spindles. The phenanthridine PJ34 kills malignant epithelial cells during mitosis and targets NuMA. PJ34 exclusively blocks the post-translational modification of NuMA in a variety of malignant epithelial cells, but not in benign cells. This blockage of the post-translational modification of NuMA affects its protein-binding capacity and causes construction faults in the mitotic spindle poles of PJ34-treated cancer cells, leading to mitotic catastrophe cell death. PJ34 is a potent PARP1 inhibitor, so its cytotoxicity in human malignant cells is exclusively independent of PARP, challenging the currently accepted notion that inhibition of PARP1 halts cancer by preventing DNA repair. Certain molecules that act as PARP1 inhibitors target other proteins and vital mechanisms in human cancer cells.
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Affiliation(s)
- Malka Cohen-Armon
- The Sackler School of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel-Aviv 69978, Israel.
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4
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Wang Y, Pleasure D, Deng W, Guo F. Therapeutic Potentials of Poly (ADP-Ribose) Polymerase 1 (PARP1) Inhibition in Multiple Sclerosis and Animal Models: Concept Revisiting. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2102853. [PMID: 34935305 PMCID: PMC8844485 DOI: 10.1002/advs.202102853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 10/12/2021] [Indexed: 05/05/2023]
Abstract
Poly (ADP-ribose) polymerase 1 (PARP1) plays a fundamental role in DNA repair and gene expression. Excessive PARP1 hyperactivation, however, has been associated with cell death. PARP1 and/or its activity are dysregulated in the immune and central nervous system of multiple sclerosis (MS) patients and animal models. Pharmacological PARP1 inhibition is shown to be protective against immune activation and disease severity in MS animal models while genetic PARP1 deficiency studies reported discrepant results. The inconsistency suggests that the function of PARP1 and PARP1-mediated PARylation may be complex and context-dependent. The article reviews PARP1 functions, discusses experimental findings and possible interpretations of PARP1 in inflammation, neuronal/axonal degeneration, and oligodendrogliopathy, three major pathological components cooperatively determining MS disease course and neurological progression, and points out future research directions. Cell type specific PARP1 manipulations are necessary for revisiting the role of PARP1 in the three pathological components prior to moving PARP1 inhibition into clinical trials for MS therapy.
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Affiliation(s)
- Yan Wang
- Department of NeurologySchool of MedicineUniversity of CaliforniaDavisCA95817USA
- Institute for Pediatric Regenerative MedicineUC Davis School of Medicine/Shriners Hospitals for ChildrenSacramentoCAUSA
| | - David Pleasure
- Department of NeurologySchool of MedicineUniversity of CaliforniaDavisCA95817USA
- Institute for Pediatric Regenerative MedicineUC Davis School of Medicine/Shriners Hospitals for ChildrenSacramentoCAUSA
| | - Wenbin Deng
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐sen UniversityGuangzhou510006China
| | - Fuzheng Guo
- Department of NeurologySchool of MedicineUniversity of CaliforniaDavisCA95817USA
- Institute for Pediatric Regenerative MedicineUC Davis School of Medicine/Shriners Hospitals for ChildrenSacramentoCAUSA
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5
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Balali E, Sandi S, Sheikhi M, Shahab S, Kaviani S. DFT and TD-DFT study of adsorption behavior of Zejula drug on surface of the B12N12 nanocluster. MAIN GROUP CHEMISTRY 2022. [DOI: 10.3233/mgc-210120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The adsorption of the Zejula drug on the surface of B12N12 nanocluster has studied using DFT and TD-DFT. The quantum calculations have performed at the M062X/6–311 + + G(d,p) level of theory in the solvent water. The adsorption of the Zejula from N13 atom on the B12N12 leads to the higher electrical conductivity due to the low Eg rather. The change of DM also displays a charge transfer between Zejula and nanocluster. The UV absorption and IR spectra were calculated. The adsorption of Zejula drug over B12N12 nanocluster in the complexes Zejula/B12N12 can be considered as a bathochromic shift. According to QTAIM analysis, -G(r)/V(r) values for B-O and B-N bonds confirming the electrostatic and partial covalent character. The values of LOL and ELF confirm that the interactions are dominated by electrostatic interaction contributions. The calculated data reveal the B12N12 nanocluster can be appropriate as a biomedical system for the delivery of Zejula drug.
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Affiliation(s)
- Ebrahim Balali
- Department of Organic Chemistry, Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Sara Sandi
- Department of Organic Chemistry, Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Masoome Sheikhi
- Young Researchers and Elite Club, Gorgan Branch, Islamic Azad University, Gorgan, Iran
| | - Siyamak Shahab
- Belarusian State University, ISEI BSU, Minsk, Republic of Belarus
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus, Minsk
- Institute of Chemistry of New Materials, National Academy of Sciences of Belarus, Minsk
| | - Sadegh Kaviani
- Research Center for Modeling and Computational Sciences, Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
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Wang Y, Zhang Y, Zhang S, Kim B, Hull VL, Xu J, Prabhu P, Gregory M, Martinez-Cerdeno V, Zhan X, Deng W, Guo F. PARP1-mediated PARylation activity is essential for oligodendroglial differentiation and CNS myelination. Cell Rep 2021; 37:109695. [PMID: 34610310 PMCID: PMC9586836 DOI: 10.1016/j.celrep.2021.109695] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/21/2021] [Accepted: 08/18/2021] [Indexed: 12/16/2022] Open
Abstract
The function of poly(ADP-ribosyl) polymerase 1 (PARP1) in myelination and remyelination of the central nervous system (CNS) remains enigmatic. Here, we report that PARP1 is an intrinsic driver for oligodendroglial development and myelination. Genetic PARP1 depletion impairs the differentiation of oligodendrocyte progenitor cells (OPCs) into oligodendrocytes and impedes CNS myelination. Mechanistically, PARP1-mediated PARylation activity is not only necessary but also sufficient for OPC differentiation. At the molecular level, we identify the RNA-binding protein Myef2 as a PARylated target, which controls OPC differentiation through the PARylation-modulated derepression of myelin protein expression. Furthermore, PARP1’s enzymatic activity is necessary for oligodendrocyte and myelin regeneration after demyelination. Together, our findings suggest that PARP1-mediated PARylation activity may be a potential therapeutic target for promoting OPC differentiation and remyelination in neurological disorders characterized by arrested OPC differentiation and remyelination failure such as multiple sclerosis. Wang et al. show that PARP1-mediated PARylation promotes oligodendroglial differentiation and regeneration. They demonstrate that PARP1 PARylates proteins relating to RNA metabolism under physiological conditions and that Myef2 is identified as one of the potential targets that mediates PARP1-regulated myelin gene expression at the posttranscriptional level during oligodendroglial development.
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Affiliation(s)
- Yan Wang
- Department of Neurology, School of Medicine, University of California, Davis, Davis, CA 95817, USA; Institute for Pediatric Regenerative Medicine (IPRM), Shriners Hospitals for Children, Sacramento, CA 95817, USA
| | - Yanhong Zhang
- Department of Neurology, School of Medicine, University of California, Davis, Davis, CA 95817, USA; Institute for Pediatric Regenerative Medicine (IPRM), Shriners Hospitals for Children, Sacramento, CA 95817, USA
| | - Sheng Zhang
- Department of Neurology, School of Medicine, University of California, Davis, Davis, CA 95817, USA; Institute for Pediatric Regenerative Medicine (IPRM), Shriners Hospitals for Children, Sacramento, CA 95817, USA
| | - Bokyung Kim
- Department of Neurology, School of Medicine, University of California, Davis, Davis, CA 95817, USA; Institute for Pediatric Regenerative Medicine (IPRM), Shriners Hospitals for Children, Sacramento, CA 95817, USA
| | - Vanessa L Hull
- Department of Neurology, School of Medicine, University of California, Davis, Davis, CA 95817, USA; Institute for Pediatric Regenerative Medicine (IPRM), Shriners Hospitals for Children, Sacramento, CA 95817, USA
| | - Jie Xu
- Institute for Pediatric Regenerative Medicine (IPRM), Shriners Hospitals for Children, Sacramento, CA 95817, USA
| | - Preeti Prabhu
- Department of Neurology, School of Medicine, University of California, Davis, Davis, CA 95817, USA; Institute for Pediatric Regenerative Medicine (IPRM), Shriners Hospitals for Children, Sacramento, CA 95817, USA
| | - Maria Gregory
- Department of Neurology, School of Medicine, University of California, Davis, Davis, CA 95817, USA; Institute for Pediatric Regenerative Medicine (IPRM), Shriners Hospitals for Children, Sacramento, CA 95817, USA
| | - Veronica Martinez-Cerdeno
- Department of Pathology and Laboratory Medicine, University of California, Davis, Davis, CA 95817, USA; Institute for Pediatric Regenerative Medicine (IPRM), Shriners Hospitals for Children, Sacramento, CA 95817, USA
| | - Xinhua Zhan
- Department of Neurology, School of Medicine, University of California, Davis, Davis, CA 95817, USA
| | - Wenbin Deng
- Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, CA 95817, USA
| | - Fuzheng Guo
- Department of Neurology, School of Medicine, University of California, Davis, Davis, CA 95817, USA; Institute for Pediatric Regenerative Medicine (IPRM), Shriners Hospitals for Children, Sacramento, CA 95817, USA.
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7
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The Modified Phenanthridine PJ34 Unveils an Exclusive Cell-Death Mechanism in Human Cancer Cells. Cancers (Basel) 2020; 12:cancers12061628. [PMID: 32575437 PMCID: PMC7352794 DOI: 10.3390/cancers12061628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 06/15/2020] [Indexed: 12/17/2022] Open
Abstract
This overview summarizes recent data disclosing the efficacy of the PARP inhibitor PJ34 in exclusive eradication of a variety of human cancer cells without impairing healthy proliferating cells. Its cytotoxic activity in cancer cells is attributed to the insertion of specific un-repairable anomalies in the structure of their mitotic spindle, leading to mitotic catastrophe cell death. This mechanism paves the way to a new concept of cancer therapy.
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Keung MY, Wu Y, Badar F, Vadgama JV. Response of Breast Cancer Cells to PARP Inhibitors Is Independent of BRCA Status. J Clin Med 2020; 9:jcm9040940. [PMID: 32235451 PMCID: PMC7231148 DOI: 10.3390/jcm9040940] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 12/12/2022] Open
Abstract
Poly (ADP-ribose) polymerase inhibitors (PARPi) have proven to be beneficial to patients with metastatic breast cancer with BRCA1/2 (BReast CAncer type 1 and type 2 genes) mutations. However, certain PARPi in pre-clinical studies have been shown to inhibit cell growth and promote the death of breast cancer cells lacking mutations in BRCA1/2. Here, we examined the inhibitory potency of 13 different PARPi in 12 breast cancer cell lines with and without BRCA-mutations using cell viability assays. The results showed that 5 of the 8 triple-negative breast cancer (TNBC) cell lines were susceptible to PARPi regardless of the BRCA-status. The estrogen receptor (ER) negative/ human epidermal growth factor receptor 2 (HER2) positive (ER-/HER2+) cells, SKBR3 and JIMT1, showed high sensitivity to Talazoparib. Especially JIMT1, which is known to be resistant to trastuzumab, was responsive to Talazoparib at 0.002 µM. Niraparib, Olaparib, and Rucaparib also demonstrated effective inhibitory potency in both advanced TNBC and ER-/HER2+ cells with and without BRCA-mutations. In contrast, a BRCA-mutant TNBC line, HCC1937, was less sensitive to Talazoparib, Niraparib, Rucaparib, and not responsive to Olaparib. Other PARPi such as UPF1069, NU1025, AZD2461, and PJ34HCl also showed potent inhibitory activity in specific breast cancer cells. Our data suggest that the benefit of PARPi therapy in breast cancer is beyond the BRCA-mutations, and equally effective on metastatic TNBC and ER-/HER2+ breast cancers.
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Affiliation(s)
- Man Yee Keung
- Division of Cancer Research and Training, Charles R. Drew University of Medicine and Science, Los Angeles, CA 90059, USA; (M.Y.K.); (F.B.)
| | - Yanyuan Wu
- Division of Cancer Research and Training, Charles R. Drew University of Medicine and Science, Los Angeles, CA 90059, USA; (M.Y.K.); (F.B.)
- David Geffen UCLA School of Medicine, Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Correspondence: (Y.W.); (J.V.V.)
| | - Francesca Badar
- Division of Cancer Research and Training, Charles R. Drew University of Medicine and Science, Los Angeles, CA 90059, USA; (M.Y.K.); (F.B.)
| | - Jaydutt V. Vadgama
- Division of Cancer Research and Training, Charles R. Drew University of Medicine and Science, Los Angeles, CA 90059, USA; (M.Y.K.); (F.B.)
- David Geffen UCLA School of Medicine, Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Correspondence: (Y.W.); (J.V.V.)
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9
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Antolin AA, Ameratunga M, Banerji U, Clarke PA, Workman P, Al-Lazikani B. The kinase polypharmacology landscape of clinical PARP inhibitors. Sci Rep 2020; 10:2585. [PMID: 32066817 PMCID: PMC7026418 DOI: 10.1038/s41598-020-59074-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 01/21/2020] [Indexed: 01/06/2023] Open
Abstract
Polypharmacology plays an important role in defining response and adverse effects of drugs. For some mechanisms, experimentally mapping polypharmacology is commonplace, although this is typically done within the same protein class. Four PARP inhibitors have been approved by the FDA as cancer therapeutics, yet a precise mechanistic rationale to guide clinicians on which to choose for a particular patient is lacking. The four drugs have largely similar PARP family inhibition profiles, but several differences at the molecular and clinical level have been reported that remain poorly understood. Here, we report the first comprehensive characterization of the off-target kinase landscape of four FDA-approved PARP drugs. We demonstrate that all four PARP inhibitors have a unique polypharmacological profile across the kinome. Niraparib and rucaparib inhibit DYRK1s, CDK16 and PIM3 at clinically achievable, submicromolar concentrations. These kinases represent the most potently inhibited off-targets of PARP inhibitors identified to date and should be investigated further to clarify their potential implications for efficacy and safety in the clinic. Moreover, broad kinome profiling is recommended for the development of PARP inhibitors as PARP-kinase polypharmacology could potentially be exploited to modulate efficacy and side-effect profiles.
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Affiliation(s)
- Albert A Antolin
- Department of Data Science, The Institute of Cancer Research, London, SM2 5NG, UK.
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK.
| | - Malaka Ameratunga
- Drug Development Unit, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Udai Banerji
- Drug Development Unit, The Institute of Cancer Research, London, SM2 5NG, UK
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Paul A Clarke
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK.
| | - Bissan Al-Lazikani
- Department of Data Science, The Institute of Cancer Research, London, SM2 5NG, UK.
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK.
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11
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Host poly(ADP-ribose) polymerases (PARPs) in acute and chronic bacterial infections. Microbes Infect 2019; 21:423-431. [DOI: 10.1016/j.micinf.2019.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/31/2019] [Accepted: 06/03/2019] [Indexed: 01/04/2023]
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12
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Visochek L, Atias D, Spektor I, Castiel A, Golan T, Cohen-Armon M. The phenanthrene derivative PJ34 exclusively eradicates human pancreatic cancer cells in xenografts. Oncotarget 2019; 10:6269-6282. [PMID: 31692907 PMCID: PMC6817443 DOI: 10.18632/oncotarget.27268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/10/2019] [Indexed: 11/25/2022] Open
Abstract
Recent reports demonstrate an exclusive eradication of a variety of human cancer cells by the modified phenanthridine PJ34. Their eradication during mitosis is attributed to PJ34 preventing NuMA clustering in the mitotic spindle poles of human malignant cells, which is crucial for their normal mitosis. Here, the effect of PJ34 is tested in cell cultures and xenografts of human pancreas ductal adenocarcinoma. Evidence is presented for a substantial reduction (80-90%) of PANC1 cancer cells in xenografts, measured 30 days after the treatment with PJ34 has been terminated. Benign cells infiltrated into the PANC1 tumors (stroma) were not affected. Growth, weight gain and behavior of the treated nude mice were not impaired during, and 30 days after the treatment with PJ34. The efficient eradication of malignant cells in human pancreas cancer xenografts presents a new model of pancreas cancer treatment.
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Affiliation(s)
- Leonid Visochek
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Dikla Atias
- Oncology Institute, Sheba Medical Center, Ramat Gan 53621, Israel
| | - Itay Spektor
- Oncology Institute, Sheba Medical Center, Ramat Gan 53621, Israel
| | - Asher Castiel
- Oncology Institute, Sheba Medical Center, Ramat Gan 53621, Israel
| | - Talia Golan
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel.,Oncology Institute, Sheba Medical Center, Ramat Gan 53621, Israel
| | - Malka Cohen-Armon
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel.,Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv 69978, Israel
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Olivés J, Mestres J. Closing the Gap Between Therapeutic Use and Mode of Action in Remedial Herbs. Front Pharmacol 2019; 10:1132. [PMID: 31632273 PMCID: PMC6785637 DOI: 10.3389/fphar.2019.01132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 08/30/2019] [Indexed: 12/17/2022] Open
Abstract
The ancient tradition of taking parts of a plant or preparing plant extracts for treating certain discomforts and maladies has long been lacking a scientific rationale to support its preparation and still widespread use in several parts of the world. In an attempt to address this challenge, we collected and integrated data connecting metabolites, plants, diseases, and proteins. A mechanistic hypothesis is generated when a metabolite is known to be present in a given plant, that plant is known to be used to treat a certain disease, that disease is known to be linked to the function of a given protein, and that protein is finally known or predicted to interact with the original metabolite. The construction of plant–protein networks from mutually connected metabolites and diseases facilitated the identification of plausible mechanisms of action for plants being used to treat analgesia, hypercholesterolemia, diarrhea, catarrh, and cough. Additional concrete examples using both experimentally known and computationally predicted, and subsequently experimentally confirmed, metabolite–protein interactions to close the connection circle between metabolites, plants, diseases, and proteins offered further proof of concept for the validity and scope of the approach to generate mode of action hypotheses for some of the therapeutic uses of remedial herbs.
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Affiliation(s)
- Joaquim Olivés
- Research Group on Systems Pharmacology, Research Programme on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Jordi Mestres
- Research Group on Systems Pharmacology, Research Programme on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute, Barcelona, Spain.,Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain
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14
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Cacciolatti C, Meyer-Ficca ML, Southwood LL, Meyer RG, Bertolotti L, Zarucco L. In vitro effects of poly(ADP-ribose) polymerase inhibitors on the production of tumor necrosis factor-α by interferon- γ - and lipopolysaccharide-stimulated peripheral blood mononuclear cells of horses. Am J Vet Res 2019; 80:663-669. [PMID: 31246122 DOI: 10.2460/ajvr.80.7.663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To evaluate effects of poly(ADP-ribose) polymerase-1 (PARP1) inhibitors on the production of tumor necrosis factor-α (TNF-α) by interferon-γ (IFN-γ)- and lipopolysaccharide (LPS)-stimulated peripheral blood mononuclear cells (PBMCs) of horses as an in vitro model of inflammation in horses. SAMPLE 1,440 samples of PBMCs from 6 healthy research horses. PROCEDURES From heparinized whole blood samples, PBMC cultures were obtained. An initial dose-response trial on 48 PBMC samples from 2 horses (24 samples each) was used to determine concentrations of IFN-γ and LPS for use as low- and high-level stimulation concentrations. Seventy-two PBMC samples from 6 horses were assigned equally to 1 of 4 PARP1 inhibition categories: no PARP1 inhibitor (PARP1 inhibition control); 2-((R)-2-methylpyrrolidin-2-yl)-1H-benzimidazole-4-carbozamide dihydrochloride (ABT888);4-(3-(1-(cyclopropanecarbonyl)piperazine-4-carbonyl)-4-fluorobenzyl)phthalazin-1(2H)-one (AZD2281); or N-(6-oxo-5,6-dihydrophenanthridin-2-yl) -N,N-dimethylacetamide hydrochloride (PJ34). Samples of PBMCs from each horse and each PARP1 inhibition category were then assigned to 1 of 3 levels of IFN-γ and LPS stimulation: none (control), low stimulation, or high stimulation. After a 24-hour incubation period, a TNF-α ELISA was used to measure TNF-α concentration in the supernatant. Results were compared across treatments and for each horse. Data were analyzed with repeated-measures ANOVA. RESULTS Median TNF-α concentration was significantly lower for PJ34-treated, high-level stimulated PBMCs than for PARP1 inhibition control, high-level stimulated PBMCs; however, no other meaningful differences in TNF-α concentration were detected among the inhibition and stimulation combinations. CONCLUSIONS AND CLINICAL RELEVANCE Findings suggested that PJ34 PARP1 inhibition may reduce TNF-α production in horses, a potential benefit in reducing inflammation and endotoxin-induced damage in horses.
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Cerisier N, Petitjean M, Regad L, Bayard Q, Réau M, Badel A, Camproux AC. High Impact: The Role of Promiscuous Binding Sites in Polypharmacology. Molecules 2019; 24:molecules24142529. [PMID: 31295958 PMCID: PMC6680532 DOI: 10.3390/molecules24142529] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 06/27/2019] [Accepted: 06/27/2019] [Indexed: 02/06/2023] Open
Abstract
The literature focuses on drug promiscuity, which is a drug’s ability to bind to several targets, because it plays an essential role in polypharmacology. However, little work has been completed regarding binding site promiscuity, even though its properties are now recognized among the key factors that impact drug promiscuity. Here, we quantified and characterized the promiscuity of druggable binding sites from protein-ligand complexes in the high quality Mother Of All Databases while using statistical methods. Most of the sites (80%) exhibited promiscuity, irrespective of the protein class. Nearly half were highly promiscuous and able to interact with various types of ligands. The corresponding pockets were rather large and hydrophobic, with high sulfur atom and aliphatic residue frequencies, but few side chain atoms. Consequently, their interacting ligands can be large, rigid, and weakly hydrophilic. The selective sites that interacted with one ligand type presented less favorable pocket properties for establishing ligand contacts. Thus, their ligands were highly adaptable, small, and hydrophilic. In the dataset, the promiscuity of the site rather than the drug mainly explains the multiple interactions between the drug and target, as most ligand types are dedicated to one site. This underlines the essential contribution of binding site promiscuity to drug promiscuity between different protein classes.
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Affiliation(s)
- Natacha Cerisier
- Université de Paris, Biologie Fonctionnelle et Adaptative, UMR 8251, CNRS, ERL U1133, INSERM, Computational Modeling of Protein Ligand Interactions, F-75013 Paris, France
| | - Michel Petitjean
- Université de Paris, Biologie Fonctionnelle et Adaptative, UMR 8251, CNRS, ERL U1133, INSERM, Computational Modeling of Protein Ligand Interactions, F-75013 Paris, France
| | - Leslie Regad
- Université de Paris, Biologie Fonctionnelle et Adaptative, UMR 8251, CNRS, ERL U1133, INSERM, Computational Modeling of Protein Ligand Interactions, F-75013 Paris, France
| | - Quentin Bayard
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, USPC, Université Paris Descartes, Université Paris Diderot, Université Paris 13, Functional Genomics of Solid Tumors Laboratory, F-75006 Paris, France
| | - Manon Réau
- Laboratoire Génomique Bioinformatique et Chimie Moléculaire, EA 7528, Conservatoire National des Arts et Métiers, F-75003 Paris, France
| | - Anne Badel
- Université de Paris, Biologie Fonctionnelle et Adaptative, UMR 8251, CNRS, ERL U1133, INSERM, Computational Modeling of Protein Ligand Interactions, F-75013 Paris, France
| | - Anne-Claude Camproux
- Université de Paris, Biologie Fonctionnelle et Adaptative, UMR 8251, CNRS, ERL U1133, INSERM, Computational Modeling of Protein Ligand Interactions, F-75013 Paris, France.
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16
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Brennecke P, Rasina D, Aubi O, Herzog K, Landskron J, Cautain B, Vicente F, Quintana J, Mestres J, Stechmann B, Ellinger B, Brea J, Kolanowski JL, Pilarski R, Orzaez M, Pineda-Lucena A, Laraia L, Nami F, Zielenkiewicz P, Paruch K, Hansen E, von Kries JP, Neuenschwander M, Specker E, Bartunek P, Simova S, Leśnikowski Z, Krauss S, Lehtiö L, Bilitewski U, Brönstrup M, Taskén K, Jirgensons A, Lickert H, Clausen MH, Andersen JH, Vicent MJ, Genilloud O, Martinez A, Nazaré M, Fecke W, Gribbon P. EU-OPENSCREEN: A Novel Collaborative Approach to Facilitate Chemical Biology. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2019; 24:398-413. [PMID: 30616481 PMCID: PMC6764006 DOI: 10.1177/2472555218816276] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/11/2018] [Accepted: 11/08/2018] [Indexed: 12/27/2022]
Abstract
Compound screening in biological assays and subsequent optimization of hits is indispensable for the development of new molecular research tools and drug candidates. To facilitate such discoveries, the European Research Infrastructure EU-OPENSCREEN was founded recently with the support of its member countries and the European Commission. Its distributed character harnesses complementary knowledge, expertise, and instrumentation in the discipline of chemical biology from 20 European partners, and its open working model ensures that academia and industry can readily access EU-OPENSCREEN's compound collection, equipment, and generated data. To demonstrate the power of this collaborative approach, this perspective article highlights recent projects from EU-OPENSCREEN partner institutions. These studies yielded (1) 2-aminoquinazolin-4(3 H)-ones as potential lead structures for new antimalarial drugs, (2) a novel lipodepsipeptide specifically inducing apoptosis in cells deficient for the pVHL tumor suppressor, (3) small-molecule-based ROCK inhibitors that induce definitive endoderm formation and can potentially be used for regenerative medicine, (4) potential pharmacological chaperones for inborn errors of metabolism and a familiar form of acute myeloid leukemia (AML), and (5) novel tankyrase inhibitors that entered a lead-to-candidate program. Collectively, these findings highlight the benefits of small-molecule screening, the plethora of assay designs, and the close connection between screening and medicinal chemistry within EU-OPENSCREEN.
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Affiliation(s)
- Philip Brennecke
- EU-OPENSCREEN, Leibniz Research
Institute for Molecular Pharmacology, Berlin, Germany
| | - Dace Rasina
- Organic Synthesis Methodology Group,
Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Oscar Aubi
- Department of Biomedicine, University of
Bergen, Bergen, Norway
| | - Katja Herzog
- EU-OPENSCREEN, Leibniz Research
Institute for Molecular Pharmacology, Berlin, Germany
| | - Johannes Landskron
- Centre for Molecular Medicine
Norway–Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - Bastien Cautain
- Fundación MEDINA, Health Sciences
Technology Park, Granada, Spain
| | | | - Jordi Quintana
- Department of Experimental and Health
Sciences, Universitat Pompeu Fabra, Barcelona, Catalunya, Spain
| | - Jordi Mestres
- Department of Experimental and Health
Sciences, Universitat Pompeu Fabra, Barcelona, Catalunya, Spain
- IMIM Hospital del Mar Medical Research
Institute, Research Program on Biomedical Informatics (GRIB), Barcelona, Spain
| | - Bahne Stechmann
- EU-OPENSCREEN, Leibniz Research
Institute for Molecular Pharmacology, Berlin, Germany
| | - Bernhard Ellinger
- Fraunhofer Institute for Molecular
Biology and Applied Ecology IME, Screening Port, Hamburg, Germany
| | - Jose Brea
- Institute for Research in Molecular
Medicine and Chronic Diseases—BioFarma Research Group, University of Santiago de
Compostela, Santiago de Compostela, Spain
| | - Jacek L. Kolanowski
- Department of Molecular Probes and
Prodrugs, Institute of Bioorganic Chemistry—Polish Academy of Sciences, Poznan,
Poland
| | - Radosław Pilarski
- Department of Molecular Probes and
Prodrugs, Institute of Bioorganic Chemistry—Polish Academy of Sciences, Poznan,
Poland
| | - Mar Orzaez
- Screening Platform, Principe Felipe
Research Center, Valencia, Spain
| | | | - Luca Laraia
- Center for Nanomedicine and
Theranostics, Department of Chemistry, Technical University of Denmark, Lyngby,
Denmark
- Technical University of Denmark,
DK-OPENSCREEN, Lyngby, Denmark
| | - Faranak Nami
- Center for Nanomedicine and
Theranostics, Department of Chemistry, Technical University of Denmark, Lyngby,
Denmark
- Technical University of Denmark,
DK-OPENSCREEN, Lyngby, Denmark
| | - Piotr Zielenkiewicz
- Department of Bioinformatics,
Institute of Biochemistry and Biophysics—Polish Academy of Sciences, Warsaw,
Poland
| | - Kamil Paruch
- Department of Chemistry—CZ-OPENSCREEN,
Masaryk University, Brno, Czech Republic
| | - Espen Hansen
- The Arctic University of Norway,
University of Tromsø, Marbio, Tromsø, Norway
| | - Jens P. von Kries
- Screening Unit, Leibniz Research
Institute for Molecular Pharmacology, Berlin, Germany
| | - Martin Neuenschwander
- Screening Unit, Leibniz Research
Institute for Molecular Pharmacology, Berlin, Germany
| | - Edgar Specker
- Medicinal Chemistry Research Group,
Leibniz Research Institute for Molecular Pharmacology, Berlin, Germany
| | - Petr Bartunek
- Institute of Molecular Genetics of the
ASCR, CZ-OPENSCREEN, Prague, Czech Republic
| | - Sarka Simova
- Institute of Molecular Genetics of the
ASCR, CZ-OPENSCREEN, Prague, Czech Republic
| | - Zbigniew Leśnikowski
- Laboratory of Molecular Virology and
Biological Chemistry, Institute of Medical Biology—Polish Academy of Sciences, Łódź,
Poland
| | - Stefan Krauss
- Department of Immunology and
Transfusion Medicine, Oslo University Hospital, Oslo, Norway
- Hybrid Technology Hub—Centre of
Excellence—Institute of Basic Medical Sciences, University of Oslo, Oslo,
Norway
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular
Medicine—Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Ursula Bilitewski
- Working Group Compound Profiling and
Screening, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Mark Brönstrup
- Department of Chemical Biology,
Helmholtz Centre for Infection Research, Brunswick, Germany
- German Center for Infection Research
(DZIF), partner site Hannover-Brunswick, Brunswick, Germany
| | - Kjetil Taskén
- Centre for Molecular Medicine
Norway–Nordic EMBL Partnership, University of Oslo, Oslo, Norway
- Department of Cancer
Immunology—Institute for Cancer Research, Oslo University Hospital, Oslo,
Norway
- K.G. Jebsen Centre for Cancer
Immunotherapy—Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- K.G. Jebsen Centre for B Cell
Malignancies—Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Aigars Jirgensons
- Organic Synthesis Methodology Group,
Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Heiko Lickert
- Institute of Diabetes and Regeneration
Research, Helmholtz Centre Munich German Research Center for Environmental Health,
Neuherberg, Germany
| | - Mads H. Clausen
- Center for Nanomedicine and
Theranostics, Department of Chemistry, Technical University of Denmark, Lyngby,
Denmark
- Technical University of Denmark,
DK-OPENSCREEN, Lyngby, Denmark
| | | | - Maria J. Vicent
- Screening Platform, Principe Felipe
Research Center, Valencia, Spain
| | - Olga Genilloud
- Fundación MEDINA, Health Sciences
Technology Park, Granada, Spain
| | - Aurora Martinez
- Department of Biomedicine, University of
Bergen, Bergen, Norway
| | - Marc Nazaré
- Medicinal Chemistry Research Group,
Leibniz Research Institute for Molecular Pharmacology, Berlin, Germany
| | | | - Philip Gribbon
- Fraunhofer Institute for Molecular
Biology and Applied Ecology IME, Screening Port, Hamburg, Germany
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17
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Antolín AA, Mestres J. Dual Inhibitors of PARPs and ROCKs. ACS OMEGA 2018; 3:12707-12712. [PMID: 30411017 PMCID: PMC6210072 DOI: 10.1021/acsomega.8b02337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 09/24/2018] [Indexed: 05/16/2023]
Abstract
Recent network and system biology analyses suggest that most complex diseases are regulated by robust and highly interconnected pathways that could be better modulated by small molecules binding to multiple biological targets. These pieces of evidence recently led to devote efforts on identifying single chemical entities that bind to two different disease-relevant targets. Here, we first predicted in silico and later confirmed in vitro that UPF 1069, a known bioactive poly(ADP-ribose) polymerase-1/2 (PARP1/2) molecule, and hydroxyfasudil, a known bioactive Rho-associated protein kinase-1/2 (ROCK1/2) molecule, have low-micromolar cross-affinity for ROCK1/2 and PARP1/2, respectively. These molecules can now be regarded as chemical seeds from which pharmacological tools could be generated to study the impact of dual inhibition of PARPs and ROCKs in preclinical models of a variety of complex diseases where both targets are involved.
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18
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Rodrigues T. Harnessing the potential of natural products in drug discovery from a cheminformatics vantage point. Org Biomol Chem 2018; 15:9275-9282. [PMID: 29085945 DOI: 10.1039/c7ob02193c] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Natural products (NPs) present a privileged source of inspiration for chemical probe and drug design. Despite the biological pre-validation of the underlying molecular architectures and their relevance in drug discovery, the poor accessibility to NPs, complexity of the synthetic routes and scarce knowledge of their macromolecular counterparts in phenotypic screens still hinder their broader exploration. Cheminformatics algorithms now provide a powerful means of circumventing the abovementioned challenges and unlocking the full potential of NPs in a drug discovery context. Herein, I discuss recent advances in the computer-assisted design of NP mimics and how artificial intelligence may accelerate future NP-inspired molecular medicine.
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Affiliation(s)
- Tiago Rodrigues
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal.
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19
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Methods to Assess the Role of Poly(ADP-Ribose) Polymerases in Regulating Mitochondrial Oxidation. Methods Mol Biol 2018; 1608:185-200. [PMID: 28695511 DOI: 10.1007/978-1-4939-6993-7_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The impact of poly(ADP-ribose) polymerase (PARP) enzymes on cellular NAD+ has been established for almost 30 years now and its sequel, the metabolic collapse of cells upon PARP overactivation is a nearly 20-year-old observation. However, in the last decade there was an enormous blooming in the understanding of the interplay between PARPs and mitochondria. Mitochondrial activity can be assessed by a comprehensive set of methods that we aim to introduce here.
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20
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Visochek L, Castiel A, Mittelman L, Elkin M, Atias D, Golan T, Izraeli S, Peretz T, Cohen-Armon M. Exclusive destruction of mitotic spindles in human cancer cells. Oncotarget 2017; 8:20813-20824. [PMID: 28209915 PMCID: PMC5400547 DOI: 10.18632/oncotarget.15343] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 01/31/2017] [Indexed: 12/15/2022] Open
Abstract
We identified target proteins modified by phenanthrenes that cause exclusive eradication of human cancer cells. The cytotoxic activity of the phenanthrenes in a variety of human cancer cells is attributed by these findings to post translational modifications of NuMA and kinesins HSET/kifC1 and kif18A. Their activity prevented the binding of NuMA to α-tubulin and kinesins in human cancer cells, and caused aberrant spindles. The most efficient cytotoxic activity of the phenanthridine PJ34, caused significantly smaller aberrant spindles with disrupted spindle poles and scattered extra-centrosomes and chromosomes. Concomitantly, PJ34 induced tumor growth arrest of human malignant tumors developed in athymic nude mice, indicating the relevance of its activity for cancer therapy.
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Affiliation(s)
- Leonid Visochek
- The Neufeld Cardiac Research Institute, Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Asher Castiel
- Cancer Research Center, Sheba Medical Center, Ramat Gan 53621, Israel
| | - Leonid Mittelman
- The Imaging Unit, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Michael Elkin
- Sharett Oncology Institute, Hadassah Medical Center, Ein-Kerem, Jerusalem 91120, Israel
| | - Dikla Atias
- Cancer Research Center, Sheba Medical Center, Ramat Gan 53621, Israel
| | - Talia Golan
- Cancer Research Center, Sheba Medical Center, Ramat Gan 53621, Israel
| | - Shai Izraeli
- Cancer Research Center, Sheba Medical Center, Ramat Gan 53621, Israel.,The Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Tamar Peretz
- Sharett Oncology Institute, Hadassah Medical Center, Ein-Kerem, Jerusalem 91120, Israel
| | - Malka Cohen-Armon
- The Neufeld Cardiac Research Institute, Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel.,Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv 69978, Israel
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21
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Hocsak E, Szabo V, Kalman N, Antus C, Cseh A, Sumegi K, Eros K, Hegedus Z, Gallyas F, Sumegi B, Racz B. PARP inhibition protects mitochondria and reduces ROS production via PARP-1-ATF4-MKP-1-MAPK retrograde pathway. Free Radic Biol Med 2017; 108:770-784. [PMID: 28457938 DOI: 10.1016/j.freeradbiomed.2017.04.018] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 04/13/2017] [Accepted: 04/16/2017] [Indexed: 12/01/2022]
Abstract
Oxidative stress induces DNA breaks and PARP-1 activation which initiates mitochondrial reactive oxygen species (ROS) production and cell death through pathways not yet identified. Here, we show the mechanism by which PARP-1 influences these processes via PARylation of activating transcription factor-4 (ATF4) responsible for MAP kinase phosphatase-1 (MKP-1) expression and thereby regulates MAP kinases. PARP inhibitor, or silencing, of PARP induced MKP-1 expression by ATF4-dependent way, and inactivated JNK and p38 MAP kinases. Additionally, it induced ATF4 expression and binding to cAMP-response element (CRE) leading to MKP-1 expression and the inactivation of MAP kinases. In contrast, PARP-1 activation induced the PARylation of ATF4 and reduced its binding to CRE sequence in vitro. CHIP-qPCR analysis showed that PARP inhibitor increased the ATF4 occupancy at the initiation site of MKP-1. In oxidative stress, PARP inhibition reduced ROS-induced cell death, suppressed mitochondrial ROS production and protected mitochondrial membrane potential on an ATF4 and MKP-1 dependent way. Basically identical results were obtained in WRL-68, A-549 and T24/83 human cell lines indicating that the aforementioned mechanism can be universal. Here, we provide the first description of PARP-1-ATF4-MKP-1-JNK/p38 MAPK retrograde pathway, which is responsible for the regulation of mitochondrial integrity, ROS production and cell death in oxidative stress, and may represent a new mechanism of PARP in cancer therapy since cancer stem cells development is JNK-dependent.
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Affiliation(s)
- Eniko Hocsak
- Departments of Biochemistry and Medical Chemistry, University of Pecs, Medical School, Pecs, Hungary; Nuclear-Mitochondrial Interactions Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
| | - Viktor Szabo
- Departments of Biochemistry and Medical Chemistry, University of Pecs, Medical School, Pecs, Hungary
| | - Nikoletta Kalman
- Departments of Biochemistry and Medical Chemistry, University of Pecs, Medical School, Pecs, Hungary
| | - Csenge Antus
- Departments of Biochemistry and Medical Chemistry, University of Pecs, Medical School, Pecs, Hungary
| | - Anna Cseh
- Departments of Biochemistry and Medical Chemistry, University of Pecs, Medical School, Pecs, Hungary
| | - Katalin Sumegi
- Departments of Biochemistry and Medical Chemistry, University of Pecs, Medical School, Pecs, Hungary
| | - Krisztian Eros
- Departments of Biochemistry and Medical Chemistry, University of Pecs, Medical School, Pecs, Hungary
| | - Zoltan Hegedus
- Departments of Biochemistry and Medical Chemistry, University of Pecs, Medical School, Pecs, Hungary; Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Ferenc Gallyas
- Departments of Biochemistry and Medical Chemistry, University of Pecs, Medical School, Pecs, Hungary; Nuclear-Mitochondrial Interactions Research Group, Hungarian Academy of Sciences, Budapest, Hungary; Szentagothai Research Center, Pecs, Hungary
| | - Balazs Sumegi
- Departments of Biochemistry and Medical Chemistry, University of Pecs, Medical School, Pecs, Hungary; Nuclear-Mitochondrial Interactions Research Group, Hungarian Academy of Sciences, Budapest, Hungary; Szentagothai Research Center, Pecs, Hungary
| | - Boglarka Racz
- Departments of Biochemistry and Medical Chemistry, University of Pecs, Medical School, Pecs, Hungary
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22
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Duran-Frigola M, Siragusa L, Ruppin E, Barril X, Cruciani G, Aloy P. Detecting similar binding pockets to enable systems polypharmacology. PLoS Comput Biol 2017; 13:e1005522. [PMID: 28662117 PMCID: PMC5490940 DOI: 10.1371/journal.pcbi.1005522] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 04/15/2017] [Indexed: 01/19/2023] Open
Abstract
In the era of systems biology, multi-target pharmacological strategies hold promise for tackling disease-related networks. In this regard, drug promiscuity may be leveraged to interfere with multiple receptors: the so-called polypharmacology of drugs can be anticipated by analyzing the similarity of binding sites across the proteome. Here, we perform a pairwise comparison of 90,000 putative binding pockets detected in 3,700 proteins, and find that 23,000 pairs of proteins have at least one similar cavity that could, in principle, accommodate similar ligands. By inspecting these pairs, we demonstrate how the detection of similar binding sites expands the space of opportunities for the rational design of drug polypharmacology. Finally, we illustrate how to leverage these opportunities in protein-protein interaction networks related to several therapeutic classes and tumor types, and in a genome-scale metabolic model of leukemia. Traditionally, the fact that most drugs are promiscuous binders has been a major concern in pharmacology, due to the occurrence of undesired off-target clinical events. In the recent years, however, the realization that many diseases are the result of complex biological processes has encouraged rethinking of drug promiscuity as a promising feature, since it is sometimes necessary to interfere with multiple receptors in order to overcome the robustness of disease-related networks. One way to identify groups of proteins that could be targeted simultaneously is to look for similar binding sites. We have massively done so for all human proteins with a known high-resolution three-dimensional structure, unveiling a vast space of ‘polypharmacology’ opportunities. Of these, we know, a great majority is not of therapeutic interest. To pinpoint promising multi-target combinations, we advocate for the use of computational tools that are able to rapidly simulate the effect of drug-target interactions on biological networks.
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Affiliation(s)
- Miquel Duran-Frigola
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | | | - Eytan Ruppin
- Department of Computer Science & Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
- School of Computer Sciences, Tel Aviv University, Tel Aviv, Israel
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Xavier Barril
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Gabriele Cruciani
- Molecular Discovery Limited, London, United Kingdom
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Patrick Aloy
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- * E-mail:
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23
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Synthesis, pharmacological evaluation and molecular docking of pyranopyrazole-linked 1,4-dihydropyridines as potent positive inotropes. Mol Divers 2017; 21:533-546. [DOI: 10.1007/s11030-017-9738-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 04/09/2017] [Indexed: 01/14/2023]
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Discovery of a New Class of Cathepsin K Inhibitors in Rhizoma Drynariae as Potential Candidates for the Treatment of Osteoporosis. Int J Mol Sci 2016; 17:ijms17122116. [PMID: 27999266 PMCID: PMC5187916 DOI: 10.3390/ijms17122116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 12/05/2016] [Accepted: 12/06/2016] [Indexed: 12/26/2022] Open
Abstract
Rhizoma Drynariae (RD), as one of the most common clinically used folk medicines, has been reported to exert potent anti-osteoporotic activity. The bioactive ingredients and mechanisms that account for its bone protective effects are under active investigation. Here we adopt a novel in silico target fishing method to reveal the target profile of RD. Cathepsin K (Ctsk) is one of the cysteine proteases that is over-expressed in osteoclasts and accounts for the increase in bone resorption in metabolic bone disorders such as postmenopausal osteoporosis. It has been the focus of target based drug discovery in recent years. We have identified two components in RD, Kushennol F and Sophoraflavanone G, that can potentially interact with Ctsk. Biological studies were performed to verify the effects of these compounds on Ctsk and its related bone resorption process, which include the use of in vitro fluorescence-based Ctsk enzyme assay, bone resorption pit formation assay, as well as Receptor Activator of Nuclear factor κB (NF-κB) ligand (RANKL)-induced osteoclastogenesis using murine RAW264.7 cells. Finally, the binding mode and stability of these two compounds that interact with Ctsk were determined by molecular docking and dynamics methods. The results showed that the in silico target fishing method could successfully identify two components from RD that show inhibitory effects on the bone resorption process related to protease Ctsk.
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Thomas C, Ji Y, Lodhi N, Kotova E, Pinnola AD, Golovine K, Makhov P, Pechenkina K, Kolenko V, Tulin AV. Non-NAD-Like poly(ADP-Ribose) Polymerase-1 Inhibitors effectively Eliminate Cancer in vivo. EBioMedicine 2016; 13:90-98. [PMID: 27727003 PMCID: PMC5264309 DOI: 10.1016/j.ebiom.2016.10.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/03/2016] [Accepted: 10/03/2016] [Indexed: 01/29/2023] Open
Abstract
The clinical potential of PARP-1 inhibitors has been recognized >10years ago, prompting intensive research on their pharmacological application in several branches of medicine, particularly in oncology. However, natural or acquired resistance of tumors to known PARP-1 inhibitors poses a serious problem for their clinical implementation. Present study aims to reignite clinical interest to PARP-1 inhibitors by introducing a new method of identifying highly potent inhibitors and presenting the largest known collection of structurally diverse inhibitors. The majority of PARP-1 inhibitors known to date have been developed as NAD competitors. NAD is utilized by many enzymes other than PARP-1, resulting in a trade-off trap between their specificity and efficacy. To circumvent this problem, we have developed a new strategy to blindly screen a small molecule library for PARP-1 inhibitors by targeting a highly specific rout of its activation. Based on this screen, we present a collection of PARP-1 inhibitors and provide their structural classification. In addition to compounds that show structural similarity to NAD or known PARP-1 inhibitors, the screen identified structurally new non-NAD-like inhibitors that block PARP-1 activity in cancer cells with greater efficacy and potency than classical PARP-1 inhibitors currently used in clinic. These non-NAD-like PARP-1 inhibitors are effective against several types of human cancer xenografts, including kidney, prostate, and breast tumors in vivo. Our pre-clinical testing of these inhibitors using laboratory animals has established a strong foundation for advancing the new inhibitors to clinical trials.
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Affiliation(s)
- Colin Thomas
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Yingbiao Ji
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Niraj Lodhi
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Elena Kotova
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | | | | | - Peter Makhov
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | | | | | - Alexei V Tulin
- Fox Chase Cancer Center, Philadelphia, PA, United States.
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Xiao YX, Yang WX. KIFC1: a promising chemotherapy target for cancer treatment? Oncotarget 2016; 7:48656-48670. [PMID: 27102297 PMCID: PMC5217046 DOI: 10.18632/oncotarget.8799] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 04/10/2016] [Indexed: 01/10/2023] Open
Abstract
The kinesin motor KIFC1 has been suggested as a potential chemotherapy target due to its critical role in clustering of the multiple centrosomes found in cancer cells. In this regard, KIFC1 seems to be non-essential in normal somatic cells which usually possess only two centrosomes. Moreover, KIFC1 is also found to initiatively drive tumor malignancy and metastasis by stabilizing a certain degree of genetic instability, delaying cell cycle and protecting cancer cell surviving signals. However, that KIFC1 also plays roles in other specific cell types complicates the question of whether it is a promising chemotherapy target for cancer treatment. For example, KIFC1 is found functionally significant in vesicular and organelle trafficking, spermiogenesis, oocyte development, embryo gestation and double-strand DNA transportation. In this review we summarize a recent collection of information so as to provide a generalized picture of ideas and mechanisms against and in favor of KIFC1 as a chemotherapy target. And we also drew the conclusion that KIFC1 is a promising chemotherapy target for some types of cancers, because the side-effects of inhibiting KIFC1 mentioned in this review are theoretically easy to avoid, while KIFC1 is functionally indispensable during mitosis and malignancy of multi-centrosome cancer cells. Further investigations of how KIFC1 is regulated throughout the mitosis in cancer cells are needed for the understanding of the pathways where KIFC1 is involved and for further exploitation of indirect KIFC1 inhibitors.
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Affiliation(s)
- Yu-Xi Xiao
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wan-Xi Yang
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, China
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Miller KA, Chaand M, Gregoire S, Yoshida T, Beck LA, Ivanov AI, Dziejman M. Characterization of V. cholerae T3SS-dependent cytotoxicity in cultured intestinal epithelial cells. Cell Microbiol 2016; 18:1857-1870. [PMID: 27302486 DOI: 10.1111/cmi.12629] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 06/01/2016] [Indexed: 12/22/2022]
Abstract
AM-19226 is a pathogenic, non-O1/non-O139 serogroup strain of Vibrio cholerae that uses a Type 3 Secretion System (T3SS) mediated mechanism to colonize host tissues and disrupt homeostasis, causing cholera. Co-culturing the Caco2-BBE human intestinal epithelial cell line with AM-19226 in the presence of bile results in rapid mammalian cell death that requires a functional T3SS. We examined the role of bile, sought to identify the mechanism, and evaluated the contributions of T3SS translocated effectors in in vitro cell death. Our results suggest that Caco2-BBE cytotoxicity does not proceed by apoptotic or necrotic mechanisms, but rather displays characteristics consistent with osmotic lysis. Cell death was preceded by disassembly of epithelial junctions and reorganization of the cortical membrane skeleton, although neither cell death nor cell-cell disruption required VopM or VopF, two effectors known to alter actin dynamics. Using deletion strains, we identified a subset of AM-19226 Vops that are required for host cell death, which were previously assigned roles in protein translocation and colonization, suggesting that they function other than to promote cytotoxicity. The collective results therefore suggest that cooperative Vop activities are required to achieve cytotoxicity in vitro, or alternatively, that translocon pores destabilize the membrane in a bile dependent manner.
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Affiliation(s)
- Kelly A Miller
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Mudit Chaand
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Stacy Gregoire
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Takeshi Yoshida
- Department of Dermatology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Lisa A Beck
- Department of Dermatology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Andrei I Ivanov
- Gastroenterology and Hepatology Division, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Michelle Dziejman
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
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Jiao K, Sahaboglu A, Zrenner E, Ueffing M, Ekström PAR, Paquet-Durand F. Efficacy of PARP inhibition in Pde6a mutant mouse models for retinitis pigmentosa depends on the quality and composition of individual human mutations. Cell Death Discov 2016; 2:16040. [PMID: 27551530 PMCID: PMC4979439 DOI: 10.1038/cddiscovery.2016.40] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 04/28/2016] [Indexed: 11/09/2022] Open
Abstract
Retinitis pigmentosa (RP), an inherited blinding disease, is caused by a variety of different mutations that affect retinal photoreceptor function and survival. So far there is neither effective treatment nor cure. We have previously shown that poly(ADP-ribose)polymerase (PARP) acts as a common and critical denominator of cell death in photoreceptors, qualifying it as a potential target for future therapeutic intervention. A significant fraction of RP-causing mutations affect the genes for the rod photoreceptor phosphodiesterase 6A (PDE6A) subunit, but it is not known whether they all engage the same death pathway. Analysing three homozygous point mutations (Pde6a R562W, D670G, and V685M) and one compound heterozygous Pde6aV685M/R562W mutation in mouse models that match human RP patients, we demonstrate excessive activation of PARP, which correlated in time with the progression of photoreceptor degeneration. The causal involvement of PARP activity in the neurodegenerative process was confirmed in organotypic retinal explant cultures treated with the PARP-selective inhibitor PJ34, using different treatment time-points and durations. Remarkably, the neuroprotective efficacy of PARP inhibition correlated inversely with the strength of the genetically induced insult, with the D670G mutant showing the best treatment effects. Our results highlight PARP as a target for neuroprotective interventions in RP caused by PDE6A mutations and are a first attempt towards personalized, genotype-matched therapy development for RP. In addition, for each of the different mutant situations, our work identifies windows of opportunity for an optimal treatment regimen for further in vivo experimentation and possibly clinical studies.
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Affiliation(s)
- K Jiao
- Cell Death Mechanisms Group, Division of Experimental Ophthalmology, Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tuebingen, Roentgenweg 11, Tuebingen 72076, Germany; Centre for Ophthalmology, The Second People's Hospital of Yunnan Province and The Fourth Affiliated Hospital of Kunming Medical University, Qingnian 176, Kunming 650021, China
| | - A Sahaboglu
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tuebingen , Tuebingen 72076, Germany
| | - E Zrenner
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen 72076, Germany; Werner Reichardt Centre for Integrative Neuroscience (CIN), University of Tuebingen, Tuebingen, Germany
| | - M Ueffing
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tuebingen , Tuebingen 72076, Germany
| | - P A R Ekström
- Division of Ophthalmology, Department of Clinical Sciences, Lund, University of Lund , Lund 22184, Sweden
| | - F Paquet-Durand
- Cell Death Mechanisms Group, Division of Experimental Ophthalmology, Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tuebingen , Roentgenweg 11, Tuebingen 72076, Germany
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Rodrigues T, Reker D, Schneider P, Schneider G. Counting on natural products for drug design. Nat Chem 2016; 8:531-41. [PMID: 27219696 DOI: 10.1038/nchem.2479] [Citation(s) in RCA: 744] [Impact Index Per Article: 93.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 02/12/2016] [Indexed: 02/08/2023]
Abstract
Natural products and their molecular frameworks have a long tradition as valuable starting points for medicinal chemistry and drug discovery. Recently, there has been a revitalization of interest in the inclusion of these chemotypes in compound collections for screening and achieving selective target modulation. Here we discuss natural-product-inspired drug discovery with a focus on recent advances in the design of synthetically tractable small molecules that mimic nature's chemistry. We highlight the potential of innovative computational tools in processing structurally complex natural products to predict their macromolecular targets and attempt to forecast the role that natural-product-derived fragments and fragment-like natural products will play in next-generation drug discovery.
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Affiliation(s)
- Tiago Rodrigues
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Daniel Reker
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Petra Schneider
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland.,inSili.com LLC, Segantinisteig 3, 8049 Zürich, Switzerland
| | - Gisbert Schneider
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
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Pratz KW, Koh BD, Patel AG, Flatten KS, Poh W, Herman JG, Dilley R, Harrell MI, Smith BD, Karp JE, Swisher EM, McDevitt MA, Kaufmann SH. Poly (ADP-Ribose) Polymerase Inhibitor Hypersensitivity in Aggressive Myeloproliferative Neoplasms. Clin Cancer Res 2016; 22:3894-902. [PMID: 26979391 DOI: 10.1158/1078-0432.ccr-15-2351] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 02/29/2016] [Indexed: 01/31/2023]
Abstract
PURPOSE DNA repair defects have been previously reported in myeloproliferative neoplasms (MPN). Inhibitors of PARP have shown activity in solid tumors with defects in homologous recombination (HR). This study was performed to assess MPN sensitivity to PARP inhibitors ex vivo EXPERIMENTAL DESIGN HR pathway integrity in circulating myeloid cells was evaluated by assessing the formation of RAD51 foci after treatment with ionizing radiation or PARP inhibitors. Sensitivity of MPN erythroid and myeloid progenitors to PARP inhibitors was evaluated using colony formation assays. RESULTS Six of 14 MPN primary samples had reduced formation of RAD51 foci after exposure to ionizing radiation, suggesting impaired HR. This phenotype was not associated with a specific MPN subtype, JAK2 mutation status, or karyotype. MPN samples showed increased sensitivity to the PARP inhibitors veliparib and olaparib compared with normal myeloid progenitors. This hypersensitivity, which was most pronounced in samples deficient in DNA damage-induced RAD51 foci, was observed predominantly in samples from patients with diagnoses of chronic myelogenous leukemia, chronic myelomonocytic leukemia, or unspecified myelodysplastic/MPN overlap syndromes. CONCLUSIONS Like other neoplasms with HR defects, MPNs exhibit PARP inhibitor hypersensitivity compared with normal marrow. These results suggest that further preclinical and possibly clinical study of PARP inhibitors in MPNs is warranted. Clin Cancer Res; 22(15); 3894-902. ©2016 AACR.
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Affiliation(s)
- Keith W Pratz
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, Maryland.
| | - Brian D Koh
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Anand G Patel
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | | | - Weijie Poh
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, Maryland
| | - James G Herman
- Division of Hematology/Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - Robert Dilley
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, Maryland
| | - Maria I Harrell
- Department of Obstetrics & Gynecology, University of Washington School of Medicine, Seattle, Washington
| | - B Douglas Smith
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, Maryland
| | - Judith E Karp
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, Maryland
| | - Elizabeth M Swisher
- Department of Obstetrics & Gynecology, University of Washington School of Medicine, Seattle, Washington
| | - Michael A McDevitt
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Scott H Kaufmann
- Department of Oncology, Mayo Clinic, Rochester, Minnesota. Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
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Shen Y, McMackin MZ, Shan Y, Raetz A, David S, Cortopassi G. Frataxin Deficiency Promotes Excess Microglial DNA Damage and Inflammation that Is Rescued by PJ34. PLoS One 2016; 11:e0151026. [PMID: 26954031 PMCID: PMC4783034 DOI: 10.1371/journal.pone.0151026] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 02/23/2016] [Indexed: 12/13/2022] Open
Abstract
An inherited deficiency in the frataxin protein causes neurodegeneration of the dorsal root ganglia and Friedreich's ataxia (FA). Frataxin deficiency leads to oxidative stress and inflammatory changes in cell and animal models; however, the cause of the inflammatory changes, and especially what causes brain microglial activation is unclear. Here we investigated: 1) the mechanism by which frataxin deficiency activates microglia, 2) whether a brain-localized inflammatory stimulus provokes a greater microglial response in FA animal models, and 3) whether an anti-inflammatory treatment improves their condition. Intracerebroventricular administration of LPS induced higher amounts of microglial activation in the FA mouse model vs controls. We also observed an increase in oxidative damage in the form of 8-oxoguanine (8-oxo-G) and the DNA repair proteins MUTYH and PARP-1 in cerebellar microglia of FA mutant mice. We hypothesized that frataxin deficiency increases DNA damage and DNA repair genes specifically in microglia, activating them. siRNA-mediated frataxin knockdown in microglial BV2 cells clearly elevated DNA damage and the expression of DNA repair genes MUTYH and PARP-1. Frataxin knockdown also induced a higher level of PARP-1 in MEF cells, and this was suppressed in MUTYH-/- knockout cells. Administration of the PARP-1 inhibitor PJ34 attenuated the microglial activation induced by intracerebroventricular injection of LPS. The combined administration of LPS and angiotensin II provoke an even stronger activation of microglia and neurobehavioral impairment. PJ34 treatment attenuated the neurobehavioral impairments in FA mice. These results suggest that the DNA repair proteins MUTYH and PARP-1 may form a pathway regulating microglial activation initiated by DNA damage, and inhibition of microglial PARP-1 induction could be an important therapeutic target in Friedreich's ataxia.
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Affiliation(s)
- Yan Shen
- Department of Molecular Biosciences, University of California Davis, Davis, California, 95616, United States of America
| | - Marissa Z. McMackin
- Department of Molecular Biosciences, University of California Davis, Davis, California, 95616, United States of America
| | - Yuxi Shan
- Department of Molecular Biosciences, University of California Davis, Davis, California, 95616, United States of America
| | - Alan Raetz
- Department of Chemistry, University of California Davis, Davis, California, 95616, United States of America
| | - Sheila David
- Department of Chemistry, University of California Davis, Davis, California, 95616, United States of America
| | - Gino Cortopassi
- Department of Molecular Biosciences, University of California Davis, Davis, California, 95616, United States of America
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Camicia R, Winkler HC, Hassa PO. Novel drug targets for personalized precision medicine in relapsed/refractory diffuse large B-cell lymphoma: a comprehensive review. Mol Cancer 2015; 14:207. [PMID: 26654227 PMCID: PMC4676894 DOI: 10.1186/s12943-015-0474-2] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 08/26/2015] [Indexed: 02/07/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is a clinically heterogeneous lymphoid malignancy and the most common subtype of non-Hodgkin's lymphoma in adults, with one of the highest mortality rates in most developed areas of the world. More than half of DLBLC patients can be cured with standard R-CHOP regimens, however approximately 30 to 40 % of patients will develop relapsed/refractory disease that remains a major cause of morbidity and mortality due to the limited therapeutic options.Recent advances in gene expression profiling have led to the identification of at least three distinct molecular subtypes of DLBCL: a germinal center B cell-like subtype, an activated B cell-like subtype, and a primary mediastinal B-cell lymphoma subtype. Moreover, recent findings have not only increased our understanding of the molecular basis of chemotherapy resistance but have also helped identify molecular subsets of DLBCL and rational targets for drug interventions that may allow for subtype/subset-specific molecularly targeted precision medicine and personalized combinations to both prevent and treat relapsed/refractory DLBCL. Novel agents such as lenalidomide, ibrutinib, bortezomib, CC-122, epratuzumab or pidilizumab used as single-agent or in combination with (rituximab-based) chemotherapy have already demonstrated promising activity in patients with relapsed/refractory DLBCL. Several novel potential drug targets have been recently identified such as the BET bromodomain protein (BRD)-4, phosphoribosyl-pyrophosphate synthetase (PRPS)-2, macrodomain-containing mono-ADP-ribosyltransferase (ARTD)-9 (also known as PARP9), deltex-3-like E3 ubiquitin ligase (DTX3L) (also known as BBAP), NF-kappaB inducing kinase (NIK) and transforming growth factor beta receptor (TGFβR).This review highlights the new insights into the molecular basis of relapsed/refractory DLBCL and summarizes the most promising drug targets and experimental treatments for relapsed/refractory DLBCL, including the use of novel agents such as lenalidomide, ibrutinib, bortezomib, pidilizumab, epratuzumab, brentuximab-vedotin or CAR T cells, dual inhibitors, as well as mechanism-based combinatorial experimental therapies. We also provide a comprehensive and updated list of current drugs, drug targets and preclinical and clinical experimental studies in DLBCL. A special focus is given on STAT1, ARTD9, DTX3L and ARTD8 (also known as PARP14) as novel potential drug targets in distinct molecular subsets of DLBCL.
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Affiliation(s)
- Rosalba Camicia
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Stem Cell Research Laboratory, NHS Blood and Transplant, Nuffield Division of Clinical, Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK.,MRC-UCL Laboratory for Molecular Cell Biology Unit, University College London, Gower Street, London, WC1E6BT, UK
| | - Hans C Winkler
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Institute of Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057, Zurich, Switzerland
| | - Paul O Hassa
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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Martínez-Bosch N, Fernández-Zapico ME, Navarro P, Yélamos J. Poly(ADP-Ribose) Polymerases: New Players in the Pathogenesis of Exocrine Pancreatic Diseases. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 186:234-41. [PMID: 26687988 DOI: 10.1016/j.ajpath.2015.09.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/04/2015] [Accepted: 09/25/2015] [Indexed: 12/20/2022]
Abstract
The poly(ADP-ribose) polymerase (PARP) enzymes were initially characterized as sensors of DNA breaks but are now known to play key roles not only in the DNA damage response but also in regulating numerous molecular processes, such as gene transcription. Furthermore, these polymerases have emerged as key players in the pathogenesis of multiple diseases, providing promising therapeutic targets for pathologies such as cardiovascular disorders, neurodegenerative diseases, and cancer. In recent years, PARPs have been implicated in the pathogenesis of pancreatitis and pancreatic cancer, and PARP inhibition has been proposed as a valuable strategy for treating these two important gastrointestinal tract disorders. For instance, in preclinical mouse models, pancreatitis was significantly attenuated after genetic or pharmacological PARP inactivation, and several clinical trials have demonstrated promising responses to PARP inhibitors in pancreatic cancer patients. In this review, we summarize the current understanding of PARP functions in these two dismal pathologies and discuss the next steps necessary to determine whether PARP inhibitors will finally make the difference in treating pancreatitis and pancreatic cancer successfully.
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Affiliation(s)
- Neus Martínez-Bosch
- Cancer Research Program, IMIM-Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Martin E Fernández-Zapico
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Pilar Navarro
- Cancer Research Program, IMIM-Hospital del Mar Medical Research Institute, Barcelona, Spain.
| | - José Yélamos
- Cancer Research Program, IMIM-Hospital del Mar Medical Research Institute, Barcelona, Spain; Network Center for Biomedical Research on Hepatic and Digestive Diseases, Madrid, Spain; Department of Immunology, Hospital del Mar, Barcelona, Spain
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Passeri D, Camaioni E, Liscio P, Sabbatini P, Ferri M, Carotti A, Giacchè N, Pellicciari R, Gioiello A, Macchiarulo A. Concepts and Molecular Aspects in the Polypharmacology of PARP-1 Inhibitors. ChemMedChem 2015; 11:1219-26. [PMID: 26424664 DOI: 10.1002/cmdc.201500391] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Indexed: 11/08/2022]
Abstract
Recent years have witnessed a renewed interest in PARP-1 inhibitors as promising anticancer agents with multifaceted functions. Particularly exciting developments include the approval of olaparib (Lynparza) for the treatment of refractory ovarian cancer in patients with BRCA1/2 mutations, and the increasing understanding of the polypharmacology of PARP-1 inhibitors. The aim of this review article is to provide the reader with a comprehensive overview of the distinct levels of the polypharmacology of PARP-1 inhibitors, including 1) inter-family polypharmacology, 2) intra-family polypharmacology, and 3) multi-signaling polypharmacology. Progress made in gaining insight into the molecular basis of these multiple target-independent and target-dependent activities of PARP-1 inhibitors are discussed, with an outlook on the potential impact that a better understanding of polypharmacology may have in aiding the explanation as to why some drug candidates work better than others in clinical settings, albeit acting on the same target with similar inhibitory potency.
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Affiliation(s)
- Daniela Passeri
- TES Pharma S.r.l., via Palmiro Togliatti 20, 06073 Corciano, Perugia, Italy
| | - Emidio Camaioni
- Dipartimento di Scienze Farmaceutiche, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Paride Liscio
- TES Pharma S.r.l., via Palmiro Togliatti 20, 06073 Corciano, Perugia, Italy
| | - Paola Sabbatini
- TES Pharma S.r.l., via Palmiro Togliatti 20, 06073 Corciano, Perugia, Italy
| | - Martina Ferri
- Dipartimento di Scienze Farmaceutiche, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Andrea Carotti
- Dipartimento di Scienze Farmaceutiche, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Nicola Giacchè
- TES Pharma S.r.l., via Palmiro Togliatti 20, 06073 Corciano, Perugia, Italy
| | | | - Antimo Gioiello
- Dipartimento di Scienze Farmaceutiche, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Antonio Macchiarulo
- Dipartimento di Scienze Farmaceutiche, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy.
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Rodrigues T, Reker D, Kunze J, Schneider P, Schneider G. Revealing the Macromolecular Targets of Fragment-Like Natural Products. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/anie.201504241] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Rodrigues T, Reker D, Kunze J, Schneider P, Schneider G. Revealing the Macromolecular Targets of Fragment-Like Natural Products. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504241] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Li Y, Lu W, Chen D, Boohaker RJ, Zhai L, Padmalayam I, Wennerberg K, Xu B, Zhang W. KIFC1 is a novel potential therapeutic target for breast cancer. Cancer Biol Ther 2015; 16:1316-22. [PMID: 26177331 DOI: 10.1080/15384047.2015.1070980] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Kinesin-like protein KIFC1, a normally nonessential kinesin motor, plays a critical role in centrosome clustering in cancer cells and is essential for the survival of cancer cells. Herein, we reported that KIFC1 expression is up-regulated in breast cancer, particularly in estrogen receptor negative, progesterone receptor negative and triple negative breast cancer, and is not associated with epidermal growth factor receptor 2 status. In addition, KIFC1 is highly expressed in all 8 tested human breast cancer cell lines, but is absent in normal human mammary epithelial cells and weakly expressed in 2 human lung fibroblast lines. Moreover, KIFC1 silencing significantly reduced breast cancer cell viability. Finally, we found that PJ34, a potent small molecule inhibitor of poly(ADP-ribose) polymerase, suppressed KIFC1 expression and induced multipolar spindle formation in breast cancer cells, and inhibited cell viability and colony formation within the same concentration range, suggesting that KIFC1 suppression by PJ34 contributes to its anti-breast cancer activity. Together, these results suggest that KIFC1 is a novel promising therapeutic target for breast cancer.
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Affiliation(s)
- Yonghe Li
- a Drug Discovery Division; Southern Research Institute ; Birmingham , AL USA
| | - Wenyan Lu
- a Drug Discovery Division; Southern Research Institute ; Birmingham , AL USA
| | - Dongquan Chen
- b Division of Preventive Medicine and Comprehensive Cancer Center; Department of Medicine; University of Alabama at Birmingham ; Birmingham , AL USA
| | - Rebecca J Boohaker
- a Drug Discovery Division; Southern Research Institute ; Birmingham , AL USA
| | - Ling Zhai
- a Drug Discovery Division; Southern Research Institute ; Birmingham , AL USA
| | - Indira Padmalayam
- a Drug Discovery Division; Southern Research Institute ; Birmingham , AL USA
| | - Krister Wennerberg
- a Drug Discovery Division; Southern Research Institute ; Birmingham , AL USA.,c Institute for Molecular Medicine Finland (FIMM); University of Helsinki ; Helsinki , Finland
| | - Bo Xu
- a Drug Discovery Division; Southern Research Institute ; Birmingham , AL USA
| | - Wei Zhang
- a Drug Discovery Division; Southern Research Institute ; Birmingham , AL USA
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Abstract
Small molecules are essential tool compounds to probe the role of proteins in biology and advance toward more efficient therapeutics. However, they are used without a complete knowledge of their selectivity across the entire proteome, at risk of confounding their effects due to unknown off-target interactions. Current state-of-the-art computational approaches to predicting the affinity profile of small molecules offer a means to anticipate potential nonobvious selectivity liabilities of chemical probes. The application of in silico target profiling on the full set of chemical probes from the NIH Molecular Libraries Program (MLP) resulted in the identification of biologically relevant in vitro affinities for proteins distantly related to the primary targets of ML006, ML123, ML141, and ML204, helping to lower the risk of their further use in chemical biology.
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Affiliation(s)
- Albert A. Antolín
- Systems
Pharmacology, Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Jordi Mestres
- Systems
Pharmacology, Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
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39
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Cleves AE, Jain AN. Chemical and protein structural basis for biological crosstalk between PPARα and COX enzymes. J Comput Aided Mol Des 2015; 29:101-12. [PMID: 25428568 PMCID: PMC4298667 DOI: 10.1007/s10822-014-9815-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 11/15/2014] [Indexed: 02/04/2023]
Abstract
We have previously validated a probabilistic framework that combined computational approaches for predicting the biological activities of small molecule drugs. Molecule comparison methods included molecular structural similarity metrics and similarity computed from lexical analysis of text in drug package inserts. Here we present an analysis of novel drug/target predictions, focusing on those that were not obvious based on known pharmacological crosstalk. Considering those cases where the predicted target was an enzyme with known 3D structure allowed incorporation of information from molecular docking and protein binding pocket similarity in addition to ligand-based comparisons. Taken together, the combination of orthogonal information sources led to investigation of a surprising predicted relationship between a transcription factor and an enzyme, specifically, PPARα and the cyclooxygenase enzymes. These predictions were confirmed by direct biochemical experiments which validate the approach and show for the first time that PPARα agonists are cyclooxygenase inhibitors.
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Affiliation(s)
- Ann E. Cleves
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA USA
| | - Ajay N. Jain
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA USA
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Antolín AA, Mestres J. Linking off-target kinase pharmacology to the differential cellular effects observed among PARP inhibitors. Oncotarget 2015; 5:3023-8. [PMID: 24632590 PMCID: PMC4102788 DOI: 10.18632/oncotarget.1814] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
PARP inhibitors hold promise as a novel class of targeted anticancer drugs. However, their true mechanism of action is still not well understood following recent reports that show marked differences in cellular effects. Here, we demonstrate that three PARP drug candidates, namely, rucaparib, veliparib, and olaparib, have a clearly different in vitro affinity profile across a panel of diverse kinases selected using a computational approach that relates proteins by ligand similarity. In this respect, rucaparib inhibits nine kinases with micromolar affinity, including PIM1, PIM2, PRKD2, DYRK1A, CDK1, CDK9, HIPK2, CK2, and ALK. In contrast, olaparib does not inhibit any of the sixteen kinases tested. In between, veliparib inhibits only two, namely, PIM1 and CDK9. The differential kinase pharmacology observed among PARP inhibitors provides a plausible explanation to their different cellular effects and offers unexplored opportunities for this drug class, but alerts also on the risk associated to transferring directly both preclinical and clinical outcomes from one PARP drug candidate to another.
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Affiliation(s)
- Albert A Antolín
- Systems Pharmacology, Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
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Rodrigues T, Lin YC, Hartenfeller M, Renner S, Lim YF, Schneider G. Repurposing de novo designed entities reveals phosphodiesterase 3B and cathepsin L modulators. Chem Commun (Camb) 2015; 51:7478-81. [DOI: 10.1039/c5cc01376c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Scaffold hopping: a computational algorithm correctly predicted the macromolecular target ofde novogenerated small molecular entities.
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Affiliation(s)
- Tiago Rodrigues
- Swiss Federal Institute of Technology (ETH)
- Department of Chemistry and Applied Biosciences
- 8093 Zürich
- Switzerland
| | - Yen-Chu Lin
- Swiss Federal Institute of Technology (ETH)
- Department of Chemistry and Applied Biosciences
- 8093 Zürich
- Switzerland
| | - Markus Hartenfeller
- Swiss Federal Institute of Technology (ETH)
- Department of Chemistry and Applied Biosciences
- 8093 Zürich
- Switzerland
- Novartis Pharma AG
| | | | - Yi Fan Lim
- Swiss Federal Institute of Technology (ETH)
- Department of Chemistry and Applied Biosciences
- 8093 Zürich
- Switzerland
| | - Gisbert Schneider
- Swiss Federal Institute of Technology (ETH)
- Department of Chemistry and Applied Biosciences
- 8093 Zürich
- Switzerland
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42
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Lechaftois M, Dreano E, Palmier B, Margaill I, Marchand-Leroux C, Bachelot-Loza C, Lerouet D. Another "string to the bow" of PJ34, a potent poly(ADP-Ribose)polymerase inhibitor: an antiplatelet effect through P2Y12 antagonism? PLoS One 2014; 9:e110776. [PMID: 25329809 PMCID: PMC4203827 DOI: 10.1371/journal.pone.0110776] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 09/16/2014] [Indexed: 11/25/2022] Open
Abstract
Background Neuro- and vasoprotective effects of poly(ADP-ribose)polymerase (PARP) inhibition have been largely documented in models of cerebral ischemia, particularly with the potent PARP inhibitor PJ34. Furthermore, after ischemic stroke, physicians are faced with incomplete tissue reperfusion and reocclusion, in which platelet activation/aggregation plays a key role. Data suggest that certain PARP inhibitors could act as antiplatelet agents. In that context, the present in vitro study investigated on human blood the potential antiplatelet effect of PJ34 and two structurally different PARP inhibitors, DPQ and INO-1001. Methods and results ADP concentrations were chosen to induce a biphasic aggregation curve resulting from the successive activation of both its receptors P2Y1 and P2Y12. In these experimental conditions, PJ34 inhibited the second phase of aggregation; this effect was reduced by incremental ADP concentrations. In addition, in line with a P2Y12 pathway inhibitory effect, PJ34 inhibited the dephosphorylation of the vasodilator stimulated phosphoprotein (VASP) in a concentration-dependent manner. Besides, PJ34 had no effect on platelet aggregation induced by collagen or PAR1 activating peptide, used at concentrations inducing a strong activation independent on secreted ADP. By contrast, DPQ and INO-1001 were devoid of any effect whatever the platelet agonist used. Conclusions We showed that, in addition to its already demonstrated beneficial effects in in vivo models of cerebral ischemia, the potent PARP inhibitor PJ34 exerts in vitro an antiplatelet effect. Moreover, this is the first study to report that PJ34 could act via a competitive P2Y12 antagonism. Thus, this antiplatelet effect could improve post-stroke reperfusion and/or prevent reocclusion, which reinforces the interest of this drug for stroke treatment.
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Affiliation(s)
- Marie Lechaftois
- EA4475-“Pharmacologie de la Circulation Cérébrale”, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, Comue Sorbonne Paris Cité, Paris, France
| | - Elise Dreano
- Inserm UMR S1140, Paris, France
- Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, Comue Sorbonne Paris Cité, Paris, France
| | - Bruno Palmier
- EA4475-“Pharmacologie de la Circulation Cérébrale”, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, Comue Sorbonne Paris Cité, Paris, France
| | - Isabelle Margaill
- EA4475-“Pharmacologie de la Circulation Cérébrale”, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, Comue Sorbonne Paris Cité, Paris, France
| | - Catherine Marchand-Leroux
- EA4475-“Pharmacologie de la Circulation Cérébrale”, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, Comue Sorbonne Paris Cité, Paris, France
| | - Christilla Bachelot-Loza
- Inserm UMR S1140, Paris, France
- Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, Comue Sorbonne Paris Cité, Paris, France
| | - Dominique Lerouet
- EA4475-“Pharmacologie de la Circulation Cérébrale”, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, Comue Sorbonne Paris Cité, Paris, France
- * E-mail:
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Martínez-Bosch N, Iglesias M, Munné-Collado J, Martínez-Cáceres C, Moreno M, Guerra C, Yélamos J, Navarro P. Parp-1 genetic ablation in Ela-myc mice unveils novel roles for Parp-1 in pancreatic cancer. J Pathol 2014; 234:214-27. [PMID: 24889936 DOI: 10.1002/path.4384] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 05/15/2014] [Accepted: 05/28/2014] [Indexed: 12/21/2022]
Abstract
Pancreatic cancer has a dismal prognosis and is currently the fourth leading cause of cancer-related death in developed countries. The inhibition of poly(ADP-ribose) polymerase-1 (Parp-1), the major protein responsible for poly(ADP-ribosy)lation in response to DNA damage, has emerged as a promising treatment for several tumour types. Here we aimed to elucidate the involvement of Parp-1 in pancreatic tumour progression. We assessed Parp-1 protein expression in normal, preneoplastic and pancreatic tumour samples from humans and from K-Ras- and c-myc-driven mouse models of pancreatic cancer. Parp-1 was highly expressed in acinar cells in normal and cancer tissues. In contrast, ductal cells expressed very low or undetectable levels of this protein, both in a normal and in a tumour context. The Parp-1 expression pattern was similar in human and mouse samples, thereby validating the use of animal models for further studies. To determine the in vivo effects of Parp-1 depletion on pancreatic cancer progression, Ela-myc-driven pancreatic tumour development was analysed in a Parp-1 knock-out background. Loss of Parp-1 resulted in increased tumour necrosis and decreased proliferation, apoptosis and angiogenesis. Interestingly, Ela-myc:Parp-1(-/-) mice displayed fewer ductal tumours than their Ela-myc:Parp-1(+/+) counterparts, suggesting that Parp-1 participates in promoting acinar-to-ductal metaplasia, a key event in pancreatic cancer initiation. Moreover, impaired macrophage recruitment can be responsible for the ADM blockade found in the Ela-myc:Parp-1(-/-) mice. Finally, molecular analysis revealed that Parp-1 modulates ADM downstream of the Stat3-MMP7 axis and is also involved in transcriptional up-regulation of the MDM2, VEGFR1 and MMP28 cancer-related genes. In conclusion, the expression pattern of Parp-1 in normal and cancer tissue and the in vivo functional effects of Parp-1 depletion point to a novel role for this protein in pancreatic carcinogenesis and shed light into the clinical use of Parp-1 inhibitors.
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Affiliation(s)
- Neus Martínez-Bosch
- Cancer Research Programme, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
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44
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Fischer JMF, Popp O, Gebhard D, Veith S, Fischbach A, Beneke S, Leitenstorfer A, Bergemann J, Scheffner M, Ferrando-May E, Mangerich A, Bürkle A. Poly(ADP-ribose)-mediated interplay of XPA and PARP1 leads to reciprocal regulation of protein function. FEBS J 2014; 281:3625-41. [PMID: 24953096 PMCID: PMC4160017 DOI: 10.1111/febs.12885] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Revised: 05/30/2014] [Accepted: 06/17/2014] [Indexed: 01/02/2023]
Abstract
Poly(ADP‐ribose) (PAR) is a complex and reversible post‐translational modification that controls protein function and localization through covalent modification of, or noncovalent binding to target proteins. Previously, we and others characterized the noncovalent, high‐affinity binding of the key nucleotide excision repair (NER) protein XPA to PAR. In the present study, we address the functional relevance of this interaction. First, we confirm that pharmacological inhibition of cellular poly(ADP‐ribosyl)ation (PARylation) impairs NER efficacy. Second, we demonstrate that the XPA–PAR interaction is mediated by specific basic amino acids within a highly conserved PAR‐binding motif, which overlaps the DNA damage‐binding protein 2 (DDB2) and transcription factor II H (TFIIH) interaction domains of XPA. Third, biochemical studies reveal a mutual regulation of PARP1 and XPA functions showing that, on the one hand, the XPA–PAR interaction lowers the DNA binding affinity of XPA, whereas, on the other hand, XPA itself strongly stimulates PARP1 enzymatic activity. Fourth, microirradiation experiments in U2OS cells demonstrate that PARP inhibition alters the recruitment properties of XPA‐green fluorescent protein to sites of laser‐induced DNA damage. In conclusion, our results reveal that XPA and PARP1 regulate each other in a reciprocal and PAR‐dependent manner, potentially acting as a fine‐tuning mechanism for the spatio‐temporal regulation of the two factors during NER.
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Affiliation(s)
- Jan M F Fischer
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, Germany
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Horvath D, Lisurek M, Rupp B, Kühne R, Specker E, von Kries J, Rognan D, Andersson CD, Almqvist F, Elofsson M, Enqvist PA, Gustavsson AL, Remez N, Mestres J, Marcou G, Varnek A, Hibert M, Quintana J, Frank R. Design of a general-purpose European compound screening library for EU-OPENSCREEN. ChemMedChem 2014; 9:2309-26. [PMID: 25044981 DOI: 10.1002/cmdc.201402126] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Indexed: 01/08/2023]
Abstract
This work describes a collaborative effort to define and apply a protocol for the rational selection of a general-purpose screening library, to be used by the screening platforms affiliated with the EU-OPENSCREEN initiative. It is designed as a standard source of compounds for primary screening against novel biological targets, at the request of research partners. Given the general nature of the potential applications of this compound collection, the focus of the selection strategy lies on ensuring chemical stability, absence of reactive compounds, screening-compliant physicochemical properties, loose compliance to drug-likeness criteria (as drug design is a major, but not exclusive application), and maximal diversity/coverage of chemical space, aimed at providing hits for a wide spectrum of drugable targets. Finally, practical availability/cost issues cannot be avoided. The main goal of this publication is to inform potential future users of this library about its conception, sources, and characteristics. The outline of the selection procedure, notably of the filtering rules designed by a large committee of European medicinal chemists and chemoinformaticians, may be of general methodological interest for the screening/medicinal chemistry community. The selection task of 200K molecules out of a pre-filtered set of 1.4M candidates was shared by five independent European research groups, each picking a subset of 40K compounds according to their own in-house methodology and expertise. An in-depth analysis of chemical space coverage of the library serves not only to characterize the collection, but also to compare the various chemoinformatics-driven selection procedures of maximal diversity sets. Compound selections contributed by various participating groups were mapped onto general-purpose self-organizing maps (SOMs) built on the basis of marketed drugs and bioactive reference molecules. In this way, the occupancy of chemical space by the EU-OPENSCREEN library could be directly compared with distributions of known bioactives of various classes. This mapping highlights the relevance of the selection and shows how the consensus reached by merging the five different 40K selections contributes to achieve this relevance. The approach also allows one to readily identify subsets of target- or target-class-oriented compounds from the EU-OPENSCREEN library to suit the needs of the diverse range of potential users. The final EU-OPENSCREEN library, assembled by merging five independent selections of 40K compounds from various expert groups, represents an excellent example of a Europe-wide collaborative effort toward the common objective of building best-in-class European open screening platforms.
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Affiliation(s)
- Dragos Horvath
- Laboratoire de Chémoinformatique, UMR 7140 CNRS (LCS) - Université de Strasbourg, 1 rue Blaise Pascal, 6700 Strasbourg (France).
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Jelinic P, Levine DA. New insights into PARP inhibitors' effect on cell cycle and homology-directed DNA damage repair. Mol Cancer Ther 2014; 13:1645-54. [PMID: 24694947 DOI: 10.1158/1535-7163.mct-13-0906-t] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In preclinical and clinical studies, olaparib and veliparib are the most represented PARP inhibitors (PARPi), which mainly target homologous DNA damage repair pathway-deficient cancer cells. Their off-target effects are not fully understood, especially with regard to cell cycle and homology-directed DNA damage repair. Our objective was to comparatively evaluate olaparib and veliparib in this context and correlate our findings with their therapeutic potential. We used a well-established direct repeat GFP (DR-GFP) reporter assay in U2OS(DR-GFP) and H1299(DR-GFP) cells and measured DNA damage repair activity upon drug treatment. Olaparib-treated U2OS(DR-GFP) cells showed a dramatic decrease in DNA damage repair versus veliparib irrespective of inhibitory potency. We demonstrate that this effect was a result of olaparib's strong effect on the cell cycle. Unlike in veliparib-treated U2OS(DR-GFP) cells, in olaparib-treated cells S-phase decreased and G(2)-phase increased sharply, indicating a G(2)-phase arrest-like state and replicative stress. This was further confirmed by upregulation of p53 and p21 and accumulation of cyclin A. Lack of the same effect in p53-null H1299(DR-GFP) cells suggested that olaparib's effect is p53 related, which was confirmed in p53-depleted U2OS(DR-GFP) and p53-null HCT116 cells. Importantly, we also demonstrate that olaparib, but not veliparib, induced a robust phosphorylation of Chk1, a crucial component of the replicative stress response pathway. Our data show olaparib and veliparib differ in their off-target effects; olaparib, unlike veliparib, mitigates DNA damage repair activity via G(2) cell-cycle arrest-like effect in a p53-dependent manner. These off-target effects may add to PARPis' anticancer properties.
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Affiliation(s)
- Petar Jelinic
- Authors' Affiliation: Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Douglas A Levine
- Authors' Affiliation: Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
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Identifying the macromolecular targets of de novo-designed chemical entities through self-organizing map consensus. Proc Natl Acad Sci U S A 2014; 111:4067-72. [PMID: 24591595 DOI: 10.1073/pnas.1320001111] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
De novo molecular design and in silico prediction of polypharmacological profiles are emerging research topics that will profoundly affect the future of drug discovery and chemical biology. The goal is to identify the macromolecular targets of new chemical agents. Although several computational tools for predicting such targets are publicly available, none of these methods was explicitly designed to predict target engagement by de novo-designed molecules. Here we present the development and practical application of a unique technique, self-organizing map-based prediction of drug equivalence relationships (SPiDER), that merges the concepts of self-organizing maps, consensus scoring, and statistical analysis to successfully identify targets for both known drugs and computer-generated molecular scaffolds. We discovered a potential off-target liability of fenofibrate-related compounds, and in a comprehensive prospective application, we identified a multitarget-modulating profile of de novo designed molecules. These results demonstrate that SPiDER may be used to identify innovative compounds in chemical biology and in the early stages of drug discovery, and help investigate the potential side effects of drugs and their repurposing options.
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48
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Stoica BA, Loane DJ, Zhao Z, Kabadi SV, Hanscom M, Byrnes KR, Faden AI. PARP-1 inhibition attenuates neuronal loss, microglia activation and neurological deficits after traumatic brain injury. J Neurotrauma 2014; 31:758-72. [PMID: 24476502 DOI: 10.1089/neu.2013.3194] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Traumatic brain injury (TBI) causes neuronal cell death as well as microglial activation and related neurotoxicity that contribute to subsequent neurological dysfunction. Poly (ADP-ribose) polymerase (PARP-1) induces neuronal cell death through activation of caspase-independent mechanisms, including release of apoptosis inducing factor (AIF), and microglial activation. Administration of PJ34, a selective PARP-1 inhibitor, reduced cell death of primary cortical neurons exposed to N-Methyl-N'-Nitro-N-Nitrosoguanidine (MNNG), a potent inducer of AIF-dependent cell death. PJ34 also attenuated lipopolysaccharide and interferon-γ-induced activation of BV2 or primary microglia, limiting NF-κB activity and iNOS expression as well as decreasing generation of reactive oxygen species and TNFα. Systemic administration of PJ34 starting as late as 24 h after controlled cortical impact resulted in improved motor function recovery in mice with TBI. Stereological analysis demonstrated that PJ34 treatment reduced the lesion volume, attenuated neuronal cell loss in the cortex and thalamus, and reduced microglial activation in the TBI cortex. PJ34 treatment did not improve cognitive performance in a Morris water maze test or reduce neuronal cell loss in the hippocampus. Overall, our data indicate that PJ34 has a significant, albeit selective, neuroprotective effect after experimental TBI, and its therapeutic effect may be from multipotential actions on neuronal cell death and neuroinflammatory pathways.
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Affiliation(s)
- Bogdan A Stoica
- 1 Department of Anesthesiology, Center for Shock, Trauma and Anesthesiology Research (STAR), National Study Center for Trauma and EMS, University of Maryland , School of Medicine, Baltimore, Maryland
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Jalencas X, Mestres J. Identification of Similar Binding Sites to Detect Distant Polypharmacology. Mol Inform 2013; 32:976-90. [PMID: 27481143 DOI: 10.1002/minf.201300082] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 07/29/2013] [Indexed: 01/19/2023]
Abstract
The ability of small molecules to interact with multiple proteins is referred to as polypharmacology. This property is often linked to the therapeutic action of drugs but it is known also to be responsible for many of their side effects. Because of its importance, the development of computational methods that can predict drug polypharmacology has become an important line of research that led recently to the identification of many novel targets for known drugs. Nowadays, the majority of these methods are based on measuring the similarity of a query molecule against the hundreds of thousands of molecules for which pharmacological data on thousands of proteins are available in public sources. However, similarity-based methods are inherently biased by the chemical coverage offered by the active molecules present in those public repositories, which limits significantly their capacity to predict interactions with proteins structurally and functionally unrelated to any of the already known targets for drugs. It is in this respect that structure-based methods aiming at identifying similar binding sites may offer an alternative complementary means to ligand-based methods for detecting distant polypharmacology. The different existing approaches to binding site detection, representation, comparison, and fragmentation are reviewed and recent successful applications presented.
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Affiliation(s)
- Xavier Jalencas
- Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Research Institute & University Pompeu Fabra, Parc de Recerca Biomèdica, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain fax: +34 93 3160550
| | - Jordi Mestres
- Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Research Institute & University Pompeu Fabra, Parc de Recerca Biomèdica, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain fax: +34 93 3160550.
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50
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Spitzmüller A, Mestres J. Prediction of the P. falciparum target space relevant to malaria drug discovery. PLoS Comput Biol 2013; 9:e1003257. [PMID: 24146604 PMCID: PMC3798273 DOI: 10.1371/journal.pcbi.1003257] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 08/20/2013] [Indexed: 11/18/2022] Open
Abstract
Malaria is still one of the most devastating infectious diseases, affecting hundreds of millions of patients worldwide. Even though there are several established drugs in clinical use for malaria treatment, there is an urgent need for new drugs acting through novel mechanisms of action due to the rapid development of resistance. Resistance emerges when the parasite manages to mutate the sequence of the drug targets to the extent that the protein can still perform its function in the parasite but can no longer be inhibited by the drug, which then becomes almost ineffective. The design of a new generation of malaria drugs targeting multiple essential proteins would make it more difficult for the parasite to develop full resistance without lethally disrupting some of its vital functions. The challenge is then to identify which set of Plasmodium falciparum proteins, among the millions of possible combinations, can be targeted at the same time by a given chemotype. To do that, we predicted first the targets of the close to 20,000 antimalarial hits identified recently in three independent phenotypic screening campaigns. All targets predicted were then projected onto the genome of P. falciparum using orthologous relationships. A total of 226 P. falciparum proteins were predicted to be hit by at least one compound, of which 39 were found to be significantly enriched by the presence and degree of affinity of phenotypically active compounds. The analysis of the chemically compatible target combinations containing at least one of those 39 targets led to the identification of a priority set of 64 multi-target profiles that can set the ground for a new generation of more robust malaria drugs.
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Affiliation(s)
- Andreas Spitzmüller
- Chemotargets SL and Systems Pharmacology, Research Programme on Biomedical Informatics (GRIB), IMIM Hospital del Mar Research Institute and Universitat Pompeu Fabra, Parc de Recerca Biomèdica, Barcelona, Catalonia, Spain
| | - Jordi Mestres
- Chemotargets SL and Systems Pharmacology, Research Programme on Biomedical Informatics (GRIB), IMIM Hospital del Mar Research Institute and Universitat Pompeu Fabra, Parc de Recerca Biomèdica, Barcelona, Catalonia, Spain
- * E-mail:
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