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Silnitsky S, Rubin SJS, Zerihun M, Qvit N. An Update on Protein Kinases as Therapeutic Targets-Part I: Protein Kinase C Activation and Its Role in Cancer and Cardiovascular Diseases. Int J Mol Sci 2023; 24:17600. [PMID: 38139428 PMCID: PMC10743896 DOI: 10.3390/ijms242417600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Protein kinases are one of the most significant drug targets in the human proteome, historically harnessed for the treatment of cancer, cardiovascular disease, and a growing number of other conditions, including autoimmune and inflammatory processes. Since the approval of the first kinase inhibitors in the late 1990s and early 2000s, the field has grown exponentially, comprising 98 approved therapeutics to date, 37 of which were approved between 2016 and 2021. While many of these small-molecule protein kinase inhibitors that interact orthosterically with the protein kinase ATP binding pocket have been massively successful for oncological indications, their poor selectively for protein kinase isozymes have limited them due to toxicities in their application to other disease spaces. Thus, recent attention has turned to the use of alternative allosteric binding mechanisms and improved drug platforms such as modified peptides to design protein kinase modulators with enhanced selectivity and other pharmacological properties. Herein we review the role of different protein kinase C (PKC) isoforms in cancer and cardiovascular disease, with particular attention to PKC-family inhibitors. We discuss translational examples and carefully consider the advantages and limitations of each compound (Part I). We also discuss the recent advances in the field of protein kinase modulators, leverage molecular docking to model inhibitor-kinase interactions, and propose mechanisms of action that will aid in the design of next-generation protein kinase modulators (Part II).
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Affiliation(s)
- Shmuel Silnitsky
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, Safed 1311502, Israel; (S.S.); (M.Z.)
| | - Samuel J. S. Rubin
- Department of Medicine, School of Medicine, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA;
| | - Mulate Zerihun
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, Safed 1311502, Israel; (S.S.); (M.Z.)
| | - Nir Qvit
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, Safed 1311502, Israel; (S.S.); (M.Z.)
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2
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Toxicity of Asciminib in Real Clinical Practice: Analysis of Side Effects and Cross-Toxicity with Tyrosine Kinase Inhibitors. Cancers (Basel) 2023; 15:cancers15041045. [PMID: 36831388 PMCID: PMC9954054 DOI: 10.3390/cancers15041045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
(1) Background: Despite the prognostic improvements achieved with tyrosine kinase inhibitors (TKIs) in chronic myeloid leukemia (CML), a minority of patients still fail TKIs. The recent introduction of asciminib may be a promising option in intolerant patients, as it is a first-in-class inhibitor with a more selective mechanism of action different from the ATP-competitive inhibition that occurs with TKIs. Therefore, our goal was to analyze toxicities shown with asciminib as well as to study cross-toxicity with previous TKIs. (2) Methods: An observational, multicenter, retrospective study was performed with data from 77 patients with CML with therapeutic failure to second-generation TKIs who received asciminib through a managed-access program (MAP) (3) Results: With a median follow-up of 13.7 months, 22 patients (28.5%) discontinued treatment: 32% (7/22) due to intolerance and 45% (10/22) due to resistance. Fifty-five percent of the patients reported adverse effects (AEs) with asciminib and eighteen percent grade 3-4. Most frequent AEs were: fatigue (18%), thrombocytopenia (17%), anemia (12%), and arthralgias (12%). None of the patients experienced cardiovascular events or occlusive arterial disease. Further, 26%, 25%, and 9% of patients required dose adjustment, temporary suspension, or definitive discontinuation of treatment, respectively. Toxicities under asciminib seemed lower than with prior TKIs for anemia, cardiovascular events, pleural/pericardial effusion, diarrhea, and edema. Cross-toxicity risk was statistically significant for thrombocytopenia, anemia, neutropenia, fatigue, vomiting, and pancreatitis. (4) Conclusion: Asciminib is a molecule with a good safety profile and with a low rate of AEs. However, despite its new mechanism of action, asciminib presents a risk of cross-toxicity with classical TKIs for some AEs.
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3
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Réa D, Hughes TP. Development of Asciminib, a Novel Allosteric Inhibitor of BCR-ABL1. Crit Rev Oncol Hematol 2022; 171:103580. [PMID: 35021069 DOI: 10.1016/j.critrevonc.2022.103580] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 12/23/2021] [Accepted: 01/05/2022] [Indexed: 01/07/2023] Open
Abstract
Chronic myeloid leukemia (CML) is driven by a translocation event between chromosomes 9 and 22, leading to the formation of a constitutively active BCR-ABL1 oncoprotein. Approved tyrosine kinase inhibitors (TKIs) for CML inhibit BCR-ABL1 by competitively targeting its adenosine triphosphate (ATP)-binding site, which significantly improves patient outcomes. However, resistance to and intolerance of TKIs remains a clinical challenge. Asciminib is a promising investigational agent in development that allosterically targets BCR-ABL1 in a non-ATP-competitive manner. It binds to the ABL1 myristoyl-binding pocket and is effective against most ABL1 kinase domain mutations that confer resistance to ATP-competitive TKIs, including the T315I mutation. This review discusses unmet needs in the current CML treatment landscape, reports clinical data from asciminib trials that support the use of single-agent asciminib as third-line therapy and beyond, and explores the potential benefit of asciminib in combination with approved TKIs in earlier lines.
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Affiliation(s)
- Delphine Réa
- Department of Hématologie, Hôpital Saint-Louis, Paris, France.
| | - Timothy P Hughes
- South Australian Health and Medical Research Institute and University of Adelaide, Adelaide, SA, Australia.
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4
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Ceramella J, Iacopetta D, Barbarossa A, Caruso A, Grande F, Bonomo MG, Mariconda A, Longo P, Carmela S, Sinicropi MS. Carbazole Derivatives as Kinase-Targeting Inhibitors for Cancer Treatment. Mini Rev Med Chem 2020; 20:444-465. [PMID: 31951166 DOI: 10.2174/1389557520666200117144701] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/01/2019] [Accepted: 10/19/2019] [Indexed: 12/11/2022]
Abstract
Protein Kinases (PKs) are a heterogeneous family of enzymes that modulate several biological pathways, including cell division, cytoskeletal rearrangement, differentiation and apoptosis. In particular, due to their crucial role during human tumorigenesis and cancer progression, PKs are ideal targets for the design and development of effective and low toxic chemotherapeutics and represent the second group of drug targets after G-protein-coupled receptors. Nowadays, several compounds have been claimed to be PKs inhibitors, and some of them, such as imatinib, erlotinib and gefitinib, have already been approved for clinical use, whereas more than 30 others are in various phases of clinical trials. Among them, some natural or synthetic carbazole-based molecules represent promising PKs inhibitors due to their capability to interfere with PK activity by different mechanisms of action including the ability to act as DNA intercalating agents, interfere with the activity of enzymes involved in DNA duplication, such as topoisomerases and telomerases, and inhibit other proteins such as cyclindependent kinases or antagonize estrogen receptors. Thus, carbazoles can be considered a promising this class of compounds to be adopted in targeted therapy of different types of cancer.
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Affiliation(s)
- Jessica Ceramella
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, (CS), Italy
| | - Domenico Iacopetta
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, (CS), Italy
| | - Alexia Barbarossa
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, (CS), Italy
| | - Anna Caruso
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, (CS), Italy
| | - Fedora Grande
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, (CS), Italy
| | | | | | - Pasquale Longo
- Department of Biology and Chemistry, University of Salerno, 84084 Fisciano, Italy
| | - Saturnino Carmela
- Department of Science, University of Basilicata, 85100 Potenza, Italy
| | - Maria Stefania Sinicropi
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, (CS), Italy
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dBMHCC: A comprehensive hepatocellular carcinoma (HCC) biomarker database provides a reliable prediction system for novel HCC phosphorylated biomarkers. PLoS One 2020; 15:e0234084. [PMID: 32497121 PMCID: PMC7272086 DOI: 10.1371/journal.pone.0234084] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 05/18/2020] [Indexed: 12/14/2022] Open
Abstract
Hepatocellular carcinoma (HCC), which is associated with an absence of obvious symptoms and poor prognosis, is the second leading cause of cancer death worldwide. Genome-wide molecular biology studies should provide biological insights into HCC development. Based on the importance of phosphorylation for signal transduction, several protein kinase inhibitors have been developed that improve the survival of cancer patients. However, a comprehensive database of HCC-related phosphorylated biomarkers (HCCPMs) and novel HCCPMs prediction platform has been lacking. We have thus constructed the dBMHCC databases to provide expression profiles, phosphorylation and drug information, and evidence type; gathered information on HCC-related pathways and their involved genes as candidate HCC biomarkers; and established a system for evaluating protein phosphorylation and HCC-related biomarkers to improve the reliability of biomarker prediction. The resulting dBMHCC contains 611 notable HCC-related genes, 234 HCC-related pathways, 17 phosphorylation-related motifs and their 255 corresponding protein kinases, 5955 HCC biomarkers, and 1077 predicted HCCPMs. Methionine adenosyltransferase 2B (MAT2B) and acireductone dioxygenase 1 (ADI1), which regulate HCC development and hepatitis C virus infection, respectively, were among the top 10 HCCPMs predicted by dBMHCC. Platelet-derived growth factor receptor alpha (PDGFRA), which had the highest evaluation score, was identified as the target of one HCC drug (Regorafenib), five cancer drugs, and four non-cancer drugs. dBMHCC is an open resource for HCC phosphorylated biomarkers, which supports researchers investigating the development of HCC and designing novel diagnosis methods and drug treatments. Database URL:http://predictor.nchu.edu.tw/dBMHCC.
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6
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Reikhardt BA, Shabanov PD. Catalytic Subunit of PKA as a Prototype of the Eukaryotic Protein Kinase Family. BIOCHEMISTRY. BIOKHIMIIA 2020; 85:409-424. [PMID: 32569549 DOI: 10.1134/s0006297920040021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 06/11/2023]
Abstract
The catalytic subunit of protein kinase A (PKAc) is conserved in all eukaryotic protein kinases. PKAc consists of two lobes that form the catalytic cleft containing the ATP-binding, peptide-binding site, and catalytic sites. During folding, PKAc secondary structures organize so that the non-polar regions form a globular core, while mobile loops and tails are exposed and can act as regulatory elements. De novo synthesized PKAc is phosphorylated at the T-loop, resulting in the formation of the active center capable of high-affinity binding of co-substrates. The ATP-molecule "sticks" the two lobes together, whereas the binding of peptide substrate completes the active center formation. The resulting catalytic triad (γ-phosphate of ATP, hydroxyl of Ser/Thr residue of the protein substrate, and Asp166 carboxyl) occupies a position optimal for catalysis. During the catalytic cycle, dynamic reorganization of polar and hydrophobic interactions ensures PKAc transition from the open to the closed conformation and vice versa. Understanding the structural basis of functioning of eukaryotic protein kinases (ePKs) is essential for successful design of ePK modulators.
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Affiliation(s)
- B A Reikhardt
- Institute of Experimental Medicine, St. Petersburg, 197376, Russia.
| | - P D Shabanov
- Institute of Experimental Medicine, St. Petersburg, 197376, Russia
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7
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Rao RN, Chanda K. An assessment study of known pyrazolopyrimidines: Chemical methodology and cellular activity. Bioorg Chem 2020; 99:103801. [PMID: 32278206 DOI: 10.1016/j.bioorg.2020.103801] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 03/22/2020] [Accepted: 03/24/2020] [Indexed: 10/24/2022]
Abstract
Heterocyclic compounds with nitrogen atom play a key role in the normal life cycle of a cell. Pyrazolopyrimidine is a privileged class of nitrogen containing fused heterocyclic compound contributing to a major portion of all lead molecules in medicinal chemistry. The thumbprint of pyrazolopyrimidine as a pharmacophore is always noticeable due to its analogy with the adenine base in DNA. Pyrazolopyrimidines are divided into five types [I, II, III, IV, V] based on the mechanism of action on the specific target conferring a wide scope of research which has accelerated the interest of researchers to investigate its biological profile. In 1956, the anti-cancer activity of pyrazolopyrimidine was evaluated for the first time with appreciable results. Since then, medicinal chemists centered their work on various methods of synthesis and evaluating the biological profile of pyrazolopyrimidine isomers. This report consists of novel methodologies followed to synthesize pyrazolopyrimidine isomers along with a note on their biological significance. To the best of our knowledge, this review article will be first of its kind to encompass different synthetic procedures along with anti-cancer, kinase inhibition, phosphodiesterase inhibition and receptor blocking activity of pyrazolopyrimidine moieties. IC50 values of potent compounds are added wherever necessary to understand the suitability of pyrazolopyrimidine skeletons for a specific biological activity.
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Affiliation(s)
- R Nishanth Rao
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632014, India
| | - Kaushik Chanda
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632014, India
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8
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Chichirau BE, Diechler S, Posselt G, Wessler S. Tyrosine Kinases in Helicobacter pylori Infections and Gastric Cancer. Toxins (Basel) 2019; 11:toxins11100591. [PMID: 31614680 PMCID: PMC6832112 DOI: 10.3390/toxins11100591] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/02/2019] [Accepted: 10/09/2019] [Indexed: 12/11/2022] Open
Abstract
Helicobacter pylori (H. pylori) has been identified as a leading cause of gastric cancer, which is one of the most frequent and malignant types of tumor. It is characterized by its rapid progression, distant metastases, and resistance to conventional chemotherapy. A number of receptor tyrosine kinases and non-receptor tyrosine kinases have been implicated in H. pylori-mediated pathogenesis and tumorigenesis. In this review, recent findings of deregulated EGFR, c-Met, JAK, FAK, Src, and c-Abl and their functions in H. pylori pathogenesis are summarized.
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Affiliation(s)
- Bianca E Chichirau
- Department of Biosciences, Paris-Lodron University of Salzburg, 5020 Salzburg, Austria.
| | - Sebastian Diechler
- Department of Biosciences, Paris-Lodron University of Salzburg, 5020 Salzburg, Austria.
| | - Gernot Posselt
- Department of Biosciences, Paris-Lodron University of Salzburg, 5020 Salzburg, Austria.
| | - Silja Wessler
- Cancer Cluster Salzburg, Department of Biosciences, Paris-Lodron University of Salzburg, 5020 Salzburg, Austria.
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9
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Tadesse S, Caldon EC, Tilley W, Wang S. Cyclin-Dependent Kinase 2 Inhibitors in Cancer Therapy: An Update. J Med Chem 2018; 62:4233-4251. [PMID: 30543440 DOI: 10.1021/acs.jmedchem.8b01469] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cyclin-dependent kinase 2 (CDK2) drives the progression of cells into the S- and M-phases of the cell cycle. CDK2 activity is largely dispensable for normal development, but it is critically associated with tumor growth in multiple cancer types. Although the role of CDK2 in tumorigenesis has been controversial, emerging evidence proposes that selective CDK2 inhibition may provide a therapeutic benefit against certain tumors, and it continues to appeal as a strategy to exploit in anticancer drug development. Several small-molecule CDK2 inhibitors have progressed to the clinical trials. However, a CDK2-selective inhibitor is yet to be discovered. Here, we discuss the latest understandings of the role of CDK2 in normal and cancer cells, review the core pharmacophores used to target CDK2, and outline strategies for the rational design of CDK2 inhibitors. We attempt to provide an outlook on how CDK2-selective inhibitors may open new avenues for cancer therapy.
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Affiliation(s)
- Solomon Tadesse
- Centre for Drug Discovery and Development , University of South Australia Cancer Research Institute , Adelaide , SA 5000 , Australia
| | - Elizabeth C Caldon
- The Kinghorn Cancer Centre , Garvan Institute of Medical Research , Darlinghurst , NSW 2010 , Australia.,St Vincent's Clinical School, UNSW Medicine , UNSW Sydney , Darlinghurst , NSW 2010 , Australia
| | - Wayne Tilley
- Adelaide Medical School , University of Adelaide , Adelaide , SA 5000 , Australia
| | - Shudong Wang
- Centre for Drug Discovery and Development , University of South Australia Cancer Research Institute , Adelaide , SA 5000 , Australia
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10
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Sharapova YA, Švedas VK. Molecular Modeling of the Binding of the Allosteric Inhibitor Optactin at a New Binding Site in Neuraminidase A from Streptococcus pneumoniae. ACTA ACUST UNITED AC 2018. [DOI: 10.3103/s0027131418050097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Malki WH, Gouda AM, Ali HEA, Al-Rousan R, Samaha D, Abdalla AN, Bustamante J, Abd Elmageed ZY, Ali HI. Structural-based design, synthesis, and antitumor activity of novel alloxazine analogues with potential selective kinase inhibition. Eur J Med Chem 2018; 152:31-52. [PMID: 29684708 DOI: 10.1016/j.ejmech.2018.04.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/12/2018] [Accepted: 04/14/2018] [Indexed: 01/09/2023]
Abstract
Protein kinases are promising therapeutic targets for cancer therapy. Here, we applied multiple approaches to optimize the potency and selectivity of our reported alloxazine scaffold. Flexible moieties at position 2 of the hetero-tricyclic system were incorporated to fit into the ATP binding site and extend to the adjacent allosteric site and selectively inhibit protein kinases. This design led to potential selective inhibition of ABL1, CDK1/Cyclin A1, FAK, and SRC kinase by 30-59%. Cytotoxicity was improved by ∼50 times for the optimized lead (10b; IC50 = 40 nM) against breast cancer (MCF-7) cells. Many compounds revealed potential cytotoxicity against ovarian (A2780) and colon carcinoma (HCT116) cells of ∼10-30 time improvement (IC50 5-17 nM). The results of the Annexin-V/PI apoptotic assay demonstrated that many compounds induced significantly early (89-146%) and a dramatically late (556-1180%) cell death in comparison to the vehicle control of MCF-7 cells. SAR indicated that 5-deazaalloxazines have a higher selectivity for Abl-1 and FAK kinases than alloxazines. The correlations between GoldScore fitness into FAK and SRC kinases and IC50 against MCF-7 and A2780 cells were considerable (R2: 0.86-0.98).
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Affiliation(s)
- Waleed H Malki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, KSA
| | - Ahmed M Gouda
- Department of Pharmaceutical Chemistry, College of Pharmacy, Umm Al-Qura University, KSA; Department of Medicinal Chemistry, College of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt
| | - Hamdy E A Ali
- Rangel College of Pharmacy, Health Science Center, Texas A&M University, Kingsville, TX 78363, United States
| | - Rabaa Al-Rousan
- The Ben and Maytee Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, TX 75799, United States
| | - Doaa Samaha
- Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, Berlin 12489, Germany; Department of Pharmaceutical Chemistry, College of Pharmacy, Helwan University, Cairo 11795, Egypt
| | - Ashraf N Abdalla
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, KSA
| | - Juan Bustamante
- Rangel College of Pharmacy, Health Science Center, Texas A&M University, Kingsville, TX 78363, United States
| | - Zakaria Y Abd Elmageed
- Rangel College of Pharmacy, Health Science Center, Texas A&M University, Kingsville, TX 78363, United States
| | - Hamed I Ali
- Rangel College of Pharmacy, Health Science Center, Texas A&M University, Kingsville, TX 78363, United States; Department of Pharmaceutical Chemistry, College of Pharmacy, Helwan University, Cairo 11795, Egypt.
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12
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Hareza A, Bakun M, Świderska B, Dudkiewicz M, Koscielny A, Bajur A, Jaworski J, Dadlez M, Pawłowski K. Phosphoproteomic insights into processes influenced by the kinase-like protein DIA1/C3orf58. PeerJ 2018; 6:e4599. [PMID: 29666759 PMCID: PMC5896498 DOI: 10.7717/peerj.4599] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 03/21/2018] [Indexed: 12/27/2022] Open
Abstract
Many kinases are still ‘orphans,’ which means knowledge about their substrates, and often also about the processes they regulate, is lacking. Here, DIA1/C3orf58, a member of a novel predicted kinase-like family, is shown to be present in the endoplasmic reticulum and to influence trafficking via the secretory pathway. Subsequently, DIA1 is subjected to phosphoproteomics analysis to cast light on its signalling pathways. A liquid chromatography–tandem mass spectrometry proteomic approach with phosphopeptide enrichment is applied to membrane fractions of DIA1-overexpressing and control HEK293T cells, and phosphosites dependent on the presence of DIA1 are elucidated. Most of these phosphosites belonged to CK2- and proline-directed kinase types. In parallel, the proteomics of proteins immunoprecipitated with DIA1 reported its probable interactors. This pilot study provides the basis for deeper studies of DIA1 signalling.
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Affiliation(s)
- Agnieszka Hareza
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland.,International Institute of Molecular and Cellular Biology, Warszawa, Poland
| | - Magda Bakun
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Bianka Świderska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Małgorzata Dudkiewicz
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland
| | - Alicja Koscielny
- International Institute of Molecular and Cellular Biology, Warszawa, Poland
| | - Anna Bajur
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland.,International Institute of Molecular and Cellular Biology, Warszawa, Poland.,Current affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jacek Jaworski
- International Institute of Molecular and Cellular Biology, Warszawa, Poland
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Krzysztof Pawłowski
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland.,Department of Translational Medicine, Clinical Sciences, Lund University, Lund, Sweden
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13
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Stroehlein AJ, Young ND, Gasser RB. Advances in kinome research of parasitic worms - implications for fundamental research and applied biotechnological outcomes. Biotechnol Adv 2018; 36:915-934. [PMID: 29477756 DOI: 10.1016/j.biotechadv.2018.02.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/15/2018] [Accepted: 02/21/2018] [Indexed: 12/17/2022]
Abstract
Protein kinases are enzymes that play essential roles in the regulation of many cellular processes. Despite expansions in the fields of genomics, transcriptomics and bioinformatics, there is limited information on the kinase complements (kinomes) of most eukaryotic organisms, including parasitic worms that cause serious diseases of humans and animals. The biological uniqueness of these worms and the draft status of their genomes pose challenges for the identification and classification of protein kinases using established tools. In this article, we provide an account of kinase biology, the roles of kinases in diseases and their importance as drug targets, and drug discovery efforts in key socioeconomically important parasitic worms. In this context, we summarise methods and resources commonly used for the curation, identification, classification and functional annotation of protein kinase sequences from draft genomes; review recent advances made in the characterisation of the worm kinomes; and discuss the implications of these advances for investigating kinase signalling and developing small-molecule inhibitors as new anti-parasitic drugs.
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Affiliation(s)
- Andreas J Stroehlein
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Neil D Young
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
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14
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Bhullar KS, Lagarón NO, McGowan EM, Parmar I, Jha A, Hubbard BP, Rupasinghe HPV. Kinase-targeted cancer therapies: progress, challenges and future directions. Mol Cancer 2018; 17:48. [PMID: 29455673 PMCID: PMC5817855 DOI: 10.1186/s12943-018-0804-2] [Citation(s) in RCA: 714] [Impact Index Per Article: 119.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 02/01/2018] [Indexed: 02/06/2023] Open
Abstract
The human genome encodes 538 protein kinases that transfer a γ-phosphate group from ATP to serine, threonine, or tyrosine residues. Many of these kinases are associated with human cancer initiation and progression. The recent development of small-molecule kinase inhibitors for the treatment of diverse types of cancer has proven successful in clinical therapy. Significantly, protein kinases are the second most targeted group of drug targets, after the G-protein-coupled receptors. Since the development of the first protein kinase inhibitor, in the early 1980s, 37 kinase inhibitors have received FDA approval for treatment of malignancies such as breast and lung cancer. Furthermore, about 150 kinase-targeted drugs are in clinical phase trials, and many kinase-specific inhibitors are in the preclinical stage of drug development. Nevertheless, many factors confound the clinical efficacy of these molecules. Specific tumor genetics, tumor microenvironment, drug resistance, and pharmacogenomics determine how useful a compound will be in the treatment of a given cancer. This review provides an overview of kinase-targeted drug discovery and development in relation to oncology and highlights the challenges and future potential for kinase-targeted cancer therapies.
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Affiliation(s)
- Khushwant S Bhullar
- Department of Pharmacology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Naiara Orrego Lagarón
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Eileen M McGowan
- Chronic Disease Solutions Team, School of Life Science, University of Technology, New South Wales, Australia
| | - Indu Parmar
- Division of Product Development, Radient Technologies, Edmonton, AB, Canada
| | - Amitabh Jha
- Department of Chemistry, Acadia University, Wolfville, NS, Canada
| | - Basil P Hubbard
- Department of Pharmacology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - H P Vasantha Rupasinghe
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada.
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada.
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15
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Zheng PP, Li J, Kros JM. Breakthroughs in modern cancer therapy and elusive cardiotoxicity: Critical research-practice gaps, challenges, and insights. Med Res Rev 2017; 38:325-376. [PMID: 28862319 PMCID: PMC5763363 DOI: 10.1002/med.21463] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 07/14/2017] [Accepted: 07/15/2017] [Indexed: 12/16/2022]
Abstract
To date, five cancer treatment modalities have been defined. The three traditional modalities of cancer treatment are surgery, radiotherapy, and conventional chemotherapy, and the two modern modalities include molecularly targeted therapy (the fourth modality) and immunotherapy (the fifth modality). The cardiotoxicity associated with conventional chemotherapy and radiotherapy is well known. Similar adverse cardiac events are resurging with the fourth modality. Aside from the conventional and newer targeted agents, even the most newly developed, immune‐based therapeutic modalities of anticancer treatment (the fifth modality), e.g., immune checkpoint inhibitors and chimeric antigen receptor (CAR) T‐cell therapy, have unfortunately led to potentially lethal cardiotoxicity in patients. Cardiac complications represent unresolved and potentially life‐threatening conditions in cancer survivors, while effective clinical management remains quite challenging. As a consequence, morbidity and mortality related to cardiac complications now threaten to offset some favorable benefits of modern cancer treatments in cancer‐related survival, regardless of the oncologic prognosis. This review focuses on identifying critical research‐practice gaps, addressing real‐world challenges and pinpointing real‐time insights in general terms under the context of clinical cardiotoxicity induced by the fourth and fifth modalities of cancer treatment. The information ranges from basic science to clinical management in the field of cardio‐oncology and crosses the interface between oncology and onco‐pharmacology. The complexity of the ongoing clinical problem is addressed at different levels. A better understanding of these research‐practice gaps may advance research initiatives on the development of mechanism‐based diagnoses and treatments for the effective clinical management of cardiotoxicity.
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Affiliation(s)
- Ping-Pin Zheng
- Cardio-Oncology Research Group, Erasmus Medical Center, Rotterdam, the Netherlands.,Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jin Li
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Johan M Kros
- Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands
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16
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Gao Y, Ye DY, Zhou WC, Chu Y. The discovery of novel benzothiazinones as highly selective non-ATP competitive glycogen synthase kinase 3β inhibitors for the treatment of ovarian cancer. Eur J Med Chem 2017; 135:370-381. [DOI: 10.1016/j.ejmech.2017.04.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 04/12/2017] [Accepted: 04/14/2017] [Indexed: 01/08/2023]
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17
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Pellerano M, Tcherniuk S, Perals C, Ngoc Van TN, Garcin E, Mahuteau-Betzer F, Teulade-Fichou MP, Morris MC. Targeting Conformational Activation of CDK2 Kinase. Biotechnol J 2017; 12. [PMID: 28430399 DOI: 10.1002/biot.201600531] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 04/20/2017] [Accepted: 04/21/2017] [Indexed: 01/12/2023]
Abstract
Cyclin-dependent kinases constitute attractive pharmacological targets for cancer therapeutics, yet inhibitors in clinical trials target the ATP-binding pocket of the CDK and therefore suffer from limited selectivity and emergence of resistance. The more recent development of allosteric inhibitors targeting conformational plasticity of protein kinases offers promising perspectives for therapeutics. In particular tampering with T-loop dynamics of CDK2 kinase would provide a selective means of inhibiting this kinase, by preventing its conformational activation. To this aim we engineered a fluorescent biosensor that specifically reports on conformational changes of CDK2 activation loop and is insensitive to ATP or ATP-competitive inhibitors, which constitutes a highly sensitive probe for identification of selective T-loop modulators. This biosensor was successfully applied to screen a library of small chemical compounds leading to discovery of a family of quinacridine analogs, which potently inhibit cancer cell proliferation, and promote accumulation of cells in S phase and G2. These compounds bind CDK2/ Cyclin A, inhibit its kinase activity, compete with substrate binding, but not with ATP, and dock onto the T-loop of CDK2. The best compound also binds CDK4 and CDK4/Cyclin D1, but not CDK1. The strategy we describe opens new doors for the discovery of a new class of allosteric CDK inhibitors for cancer therapeutics.
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Affiliation(s)
- Morgan Pellerano
- Institut des Biomolécules Max Mousseron, Université de Montpellier, Faculté de Pharmacie, Montpellier, France
| | - Sergey Tcherniuk
- Institut des Biomolécules Max Mousseron, Université de Montpellier, Faculté de Pharmacie, Montpellier, France
| | - Corine Perals
- Centre de Physiopathologie de Toulouse Purpan, Université de Toulouse Paul Sabatier, CHU Purpan, Toulouse Cedex 3, France
| | - Thi Nhu Ngoc Van
- Institut des Biomolécules Max Mousseron, Université de Montpellier, Faculté de Pharmacie, Montpellier, France
| | - Elsa Garcin
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, USA
| | | | | | - May C Morris
- Institut des Biomolécules Max Mousseron, Université de Montpellier, Faculté de Pharmacie, Montpellier, France
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18
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Ismail NS, Ali GM, Ibrahim DA, Elmetwali AM. Medicinal attributes of pyrazolo[1,5-a]pyrimidine based scaffold derivatives targeting kinases as anticancer agents. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2016. [DOI: 10.1016/j.fjps.2016.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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19
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Lu F, Luo G, Qiao L, Jiang L, Li G, Zhang Y. Virtual Screening for Potential Allosteric Inhibitors of Cyclin-Dependent Kinase 2 from Traditional Chinese Medicine. Molecules 2016; 21:molecules21091259. [PMID: 27657032 PMCID: PMC6274045 DOI: 10.3390/molecules21091259] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/01/2016] [Accepted: 09/17/2016] [Indexed: 01/16/2023] Open
Abstract
Cyclin-dependent kinase 2 (CDK2), a member of Cyclin-dependent kinases (CDKs), plays an important role in cell division and DNA replication. It is regarded as a desired target to treat cancer and tumor by interrupting aberrant cell proliferation. Compared to lower subtype selectivity of CDK2 ATP-competitive inhibitors, CDK2 allosteric inhibitor with higher subtype selectivity has been used to treat CDK2-related diseases. Recently, the first crystal structure of CDK2 with allosteric inhibitor has been reported, which provides new opportunities to design pure allosteric inhibitors of CDK2. The binding site of the ATP-competition inhibitors and the allosteric inhibitors are partially overlapped in space position, so the same compound might interact with the two binding sites. Thus a novel screening strategy was essential for the discovery of pure CDK2 allosteric inhibitors. In this study, pharmacophore and molecular docking were used to screen potential CDK2 allosteric inhibitors and ATP-competition inhibitors from Traditional Chinese Medicine (TCM). In the docking result of the allosteric site, the compounds which can act with the CDK2 ATP site were discarded, and the remaining compounds were regarded as the potential pure allosteric inhibitors. Among the results, prostaglandin E1 and nordihydroguaiaretic acid (NDGA) were available and their growth inhibitory effect on human HepG2 cell lines was determined by MTT assay. The two compounds could substantially inhibit the growth of HepG2 cell lines with an estimated IC50 of 41.223 μmol/L and 45.646 μmol/L. This study provides virtual screening strategy of allosteric compounds and a reliable method to discover potential pure CDK2 allosteric inhibitors from TCM. Prostaglandin E1 and NDGA could be regarded as promising candidates for CDK2 allosteric inhibitors.
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Affiliation(s)
- Fang Lu
- Beijing Key Laboratory of TCM Foundation and New Drug Research, School of Chinese Material Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Ganggang Luo
- Beijing Key Laboratory of TCM Foundation and New Drug Research, School of Chinese Material Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Liansheng Qiao
- Beijing Key Laboratory of TCM Foundation and New Drug Research, School of Chinese Material Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Ludi Jiang
- Beijing Key Laboratory of TCM Foundation and New Drug Research, School of Chinese Material Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Gongyu Li
- Beijing Key Laboratory of TCM Foundation and New Drug Research, School of Chinese Material Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Yanling Zhang
- Beijing Key Laboratory of TCM Foundation and New Drug Research, School of Chinese Material Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
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20
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Christmann-Franck S, van Westen GJP, Papadatos G, Beltran Escudie F, Roberts A, Overington JP, Domine D. Unprecedently Large-Scale Kinase Inhibitor Set Enabling the Accurate Prediction of Compound-Kinase Activities: A Way toward Selective Promiscuity by Design? J Chem Inf Model 2016; 56:1654-75. [PMID: 27482722 PMCID: PMC5039764 DOI: 10.1021/acs.jcim.6b00122] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Drug discovery programs frequently target members of the human kinome and try to identify small molecule protein kinase inhibitors, primarily for cancer treatment, additional indications being increasingly investigated. One of the challenges is controlling the inhibitors degree of selectivity, assessed by in vitro profiling against panels of protein kinases. We manually extracted, compiled, and standardized such profiles published in the literature: we collected 356 908 data points corresponding to 482 protein kinases, 2106 inhibitors, and 661 patents. We then analyzed this data set in terms of kinome coverage, results reproducibility, popularity, and degree of selectivity of both kinases and inhibitors. We used the data set to create robust proteochemometric models capable of predicting kinase activity (the ligand-target space was modeled with an externally validated RMSE of 0.41 ± 0.02 log units and R02 0.74 ± 0.03), in order to account for missing or unreliable measurements. The influence on the prediction quality of parameters such as number of measurements, Murcko scaffold frequency or inhibitor type was assessed. Interpretation of the models enabled to highlight inhibitors and kinases properties correlated with higher affinities, and an analysis in the context of kinases crystal structures was performed. Overall, the models quality allows the accurate prediction of kinase-inhibitor activities and their structural interpretation, thus paving the way for the rational design of compounds with a targeted selectivity profile.
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Affiliation(s)
| | - Gerard J P van Westen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SD, U.K
| | - George Papadatos
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SD, U.K
| | | | | | - John P Overington
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SD, U.K
| | - Daniel Domine
- Merck Serono , Chemin des Mines 9, 1202 Genève, Switzerland
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21
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Khattab M, Wang F, Clayton AHA. UV-Vis spectroscopy and solvatochromism of the tyrosine kinase inhibitor AG-1478. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 164:128-132. [PMID: 27092736 DOI: 10.1016/j.saa.2016.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/24/2016] [Accepted: 04/04/2016] [Indexed: 06/05/2023]
Abstract
The effect of twenty-one solvents on the UV-Vis spectrum of the tyrosine kinase inhibitor AG-1478 was investigated. The absorption spectrum in the range 300-360nm consisted of two partially overlapping bands at approximately 340nm and 330nm. The higher energy absorption band was more sensitive to solvent and exhibited a peak position that varied from 327nm to 336nm, while the lower energy absorption band demonstrated a change in peak position from 340nm to 346nm in non-chlorinated solvents. The fluorescence spectrum of AG-1478 was particularly sensitive to solvent. The wavelength of peak intensity varied from 409nm to 495nm with the corresponding Stokes shift in the range of 64nm to 155nm (4536cm(-1) to 9210cm(-1)). We used a number of methods to assess the relationship between spectroscopic properties and solvent properties. The detailed analysis revealed that for aprotic solvents, the peak position of the emission spectrum in wavenumber scale correlated with the polarity (dielectric constant or ET(30)) of the solvent. In protic solvents, a better correlation was observed between the hydrogen bonding power of the solvent and the position of the emission spectrum. Moreover, the fluorescence quantum yields were larger in aprotic solvents as compared to protic solvents. This analysis underscores the importance of polarity and hydrogen-bonding environment on the spectroscopic properties of AG-1478. These studies will assume relevance in understanding the interaction of AG-1478 in vitro and in vivo.
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Affiliation(s)
- Muhammad Khattab
- Centre for Micro-Photonics, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Victoria 3122, Australia.
| | - Feng Wang
- Molecular Model Discovery Laboratory, Department of Chemistry and Biotechnology, School of Science, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Victoria 3122, Australia.
| | - Andrew H A Clayton
- Centre for Micro-Photonics, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Victoria 3122, Australia.
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22
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From Drug Screening to Target Deconvolution: a Target-Based Drug Discovery Pipeline Using Leishmania Casein Kinase 1 Isoform 2 To Identify Compounds with Antileishmanial Activity. Antimicrob Agents Chemother 2016; 60:2822-33. [PMID: 26902771 DOI: 10.1128/aac.00021-16] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 02/18/2016] [Indexed: 01/28/2023] Open
Abstract
Existing therapies for leishmaniases present significant limitations, such as toxic side effects, and are rendered inefficient by parasite resistance. It is of utmost importance to develop novel drugs targeting Leishmania that take these two limitations into consideration. We thus chose a target-based approach using an exoprotein kinase, Leishmania casein kinase 1.2 (LmCK1.2) that was recently shown to be essential for intracellular parasite survival and infectivity. We developed a four-step pipeline to identify novel selective antileishmanial compounds. In step 1, we screened 5,018 compounds from kinase-biased libraries with Leishmania and mammalian CK1 in order to identify hit compounds and assess their specificity. For step 2, we selected 88 compounds among those with the lowest 50% inhibitory concentration to test their biological activity on host-free parasites using a resazurin reduction assay and on intramacrophagic amastigotes using a high content phenotypic assay. Only 75 compounds showed antileishmanial activity and were retained for step 3 to evaluate their toxicity against mouse macrophages and human cell lines. The four compounds that displayed a selectivity index above 10 were then assessed for their affinity to LmCK1.2 using a target deconvolution strategy in step 4. Finally, we retained two compounds, PP2 and compound 42, for which LmCK1.2 seems to be the primary target. Using this four-step pipeline, we identify from several thousand molecules, two lead compounds with a selective antileishmanial activity.
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23
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Mehdizadeh A, Somi MH, Darabi M, Jabbarpour-Bonyadi M. Extracellular signal-regulated kinase 1 and 2 in cancer therapy: a focus on hepatocellular carcinoma. Mol Biol Rep 2016; 43:107-16. [DOI: 10.1007/s11033-016-3943-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 01/05/2016] [Indexed: 12/30/2022]
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24
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McSkimming DI, Dastgheib S, Talevich E, Narayanan A, Katiyar S, Taylor SS, Kochut K, Kannan N. ProKinO: a unified resource for mining the cancer kinome. Hum Mutat 2015; 36:175-86. [PMID: 25382819 PMCID: PMC4342772 DOI: 10.1002/humu.22726] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 10/21/2014] [Indexed: 12/31/2022]
Abstract
Protein kinases represent a large and diverse family of evolutionarily related proteins that are abnormally regulated in human cancers. Although genome sequencing studies have revealed thousands of variants in protein kinases, translating "big" genomic data into biological knowledge remains a challenge. Here, we describe an ontological framework for integrating and conceptualizing diverse forms of information related to kinase activation and regulatory mechanisms in a machine readable, human understandable form. We demonstrate the utility of this framework in analyzing the cancer kinome, and in generating testable hypotheses for experimental studies. Through the iterative process of aggregate ontology querying, hypothesis generation and experimental validation, we identify a novel mutational hotspot in the αC-β4 loop of the kinase domain and demonstrate the functional impact of the identified variants in epidermal growth factor receptor (EGFR) constitutive activity and inhibitor sensitivity. We provide a unified resource for the kinase and cancer community, ProKinO, housed at http://vulcan.cs.uga.edu/prokino.
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25
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26
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Brummond KM, Kocsis LS. Intramolecular didehydro-Diels-Alder reaction and its impact on the structure-function properties of environmentally sensitive fluorophores. Acc Chem Res 2015. [PMID: 26207414 DOI: 10.1021/acs.accounts.5b00126] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Reaction discovery plays a vital role in accessing new chemical entities and materials possessing important function.1 In this Account, we delineate our reaction discovery program regarding the [4 + 2] cycloaddition reaction of styrene-ynes. In particular, we highlight our studies that lead to the realization of the diverging reaction mechanisms of the intramolecular didehydro-Diels-Alder (IMDDA) reaction to afford dihydronaphthalene and naphthalene products. Formation of the former involves an intermolecular hydrogen atom abstraction and isomerization, whereas the latter is formed via an unexpected elimination of H2. Forming aromatic compounds by a unimolecular elimination of H2 offers an environmentally benign alternative to typical oxidation protocols. We also include in this Account ongoing work focused on expanding the scope of this reaction, mainly its application to the preparation of cyclopenta[b]naphthalenes. Finally, we showcase the synthetic utility of the IMDDA reaction by preparing novel environmentally sensitive fluorophores. The choice to follow this path was largely influenced by the impact this reaction could have on our understanding of the structure-function relationships of these molecular sensors by taking advantage of a de novo construction and functionalization of the aromatic portion of these compounds. We were also inspired by the fact that, despite the advances that have been made in the construction of small molecule fluorophores, access to rationally designed fluorescent probes or sensors possessing varied and tuned photophysical, spectral, and chemical properties are still needed. To this end, we report our studies to correlate fluorophore structure with photophysical property relationships for a series of solvatochromic PRODAN analogs and viscosity-sensitive cyanoacrylate analogs. The versatility of this de novo strategy for fluorophore synthesis was demonstrated by showing that a number of functional groups could be installed at various locations, including handles for eventual biomolecule attachment or water-solubilizing groups. Further, biothiol sensors were designed, and we expect these to be of general utility for the study of lipid dynamics in cellular membranes and for the detection of protein-binding interactions, ideal applications for these relatively hydrophobic fluorophores. Future studies will be directed toward expanding this chemistry-driven approach to the rational preparation of fluorophores with enhanced photophysical and chemical properties for application in biological systems.
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Affiliation(s)
- Kay M. Brummond
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15206, United States
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27
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Basnet SKC, Diab S, Schmid R, Yu M, Yang Y, Gillam TA, Teo T, Li P, Peat T, Albrecht H, Wang S. Identification of a Highly Conserved Allosteric Binding Site on Mnk1 and Mnk2. Mol Pharmacol 2015; 88:935-48. [PMID: 26268528 DOI: 10.1124/mol.115.100131] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/11/2015] [Indexed: 12/19/2022] Open
Abstract
Elevated levels of phosphorylated eukaryotic initiation factor 4E (eIF4E) have been implicated in many tumor types, and mitogen activated protein kinase-interacting kinases (Mnks) are the only known kinases that phosphorylate eIF4E at Ser209. The phosphorylation of eIF4E is essential for oncogenic transformation but is of no significance to normal growth and development. Pharmacological inhibition of Mnks therefore provides a nontoxic and effective strategy for cancer therapy. However, a lack of specific Mnk inhibitors has confounded pharmacological target validation and clinical development. Herein, we report the identification of a novel series of Mnk inhibitors and their binding modes. A systematic workflow has been established to distinguish between type III and type I/II inhibitors. A selection of 66 compounds was tested for Mnk1 and Mnk2 inhibition, and 9 out of 20 active compounds showed type III interaction with an allosteric site of the proteins. Most of the type III inhibitors exhibited dual Mnk1 and Mnk2 activities and demonstrated potent antiproliferative properties against the MV4-11 acute myeloid leukemia cell line. Interestingly, ATP-/substrate-competitive inhibitors were found to be highly selective for Mnk2, with little or no activity for Mnk1. Our study suggests that Mnk1 and Mnk2 share a common structure of the allosteric inhibitory binding site but possess different structural features of the ATP catalytic domain. The findings will assist in the future design and development of Mnk targeted anticancer therapeutics.
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Affiliation(s)
- Sunita K C Basnet
- Centre for Drug Discovery and Development, Sansom Institute for Health Research, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia (S.K.C.B., S.D., R.S., M.Y., Y.Y., T.A.G., T.T., P.L., H.A., S.W.); and CSIRO Biosciences Program, Parkville, Victoria, Australia (T.P.)
| | - Sarah Diab
- Centre for Drug Discovery and Development, Sansom Institute for Health Research, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia (S.K.C.B., S.D., R.S., M.Y., Y.Y., T.A.G., T.T., P.L., H.A., S.W.); and CSIRO Biosciences Program, Parkville, Victoria, Australia (T.P.)
| | - Raffaella Schmid
- Centre for Drug Discovery and Development, Sansom Institute for Health Research, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia (S.K.C.B., S.D., R.S., M.Y., Y.Y., T.A.G., T.T., P.L., H.A., S.W.); and CSIRO Biosciences Program, Parkville, Victoria, Australia (T.P.)
| | - Mingfeng Yu
- Centre for Drug Discovery and Development, Sansom Institute for Health Research, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia (S.K.C.B., S.D., R.S., M.Y., Y.Y., T.A.G., T.T., P.L., H.A., S.W.); and CSIRO Biosciences Program, Parkville, Victoria, Australia (T.P.)
| | - Yuchao Yang
- Centre for Drug Discovery and Development, Sansom Institute for Health Research, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia (S.K.C.B., S.D., R.S., M.Y., Y.Y., T.A.G., T.T., P.L., H.A., S.W.); and CSIRO Biosciences Program, Parkville, Victoria, Australia (T.P.)
| | - Todd Alexander Gillam
- Centre for Drug Discovery and Development, Sansom Institute for Health Research, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia (S.K.C.B., S.D., R.S., M.Y., Y.Y., T.A.G., T.T., P.L., H.A., S.W.); and CSIRO Biosciences Program, Parkville, Victoria, Australia (T.P.)
| | - Theodosia Teo
- Centre for Drug Discovery and Development, Sansom Institute for Health Research, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia (S.K.C.B., S.D., R.S., M.Y., Y.Y., T.A.G., T.T., P.L., H.A., S.W.); and CSIRO Biosciences Program, Parkville, Victoria, Australia (T.P.)
| | - Peng Li
- Centre for Drug Discovery and Development, Sansom Institute for Health Research, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia (S.K.C.B., S.D., R.S., M.Y., Y.Y., T.A.G., T.T., P.L., H.A., S.W.); and CSIRO Biosciences Program, Parkville, Victoria, Australia (T.P.)
| | - Tom Peat
- Centre for Drug Discovery and Development, Sansom Institute for Health Research, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia (S.K.C.B., S.D., R.S., M.Y., Y.Y., T.A.G., T.T., P.L., H.A., S.W.); and CSIRO Biosciences Program, Parkville, Victoria, Australia (T.P.)
| | - Hugo Albrecht
- Centre for Drug Discovery and Development, Sansom Institute for Health Research, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia (S.K.C.B., S.D., R.S., M.Y., Y.Y., T.A.G., T.T., P.L., H.A., S.W.); and CSIRO Biosciences Program, Parkville, Victoria, Australia (T.P.)
| | - Shudong Wang
- Centre for Drug Discovery and Development, Sansom Institute for Health Research, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia (S.K.C.B., S.D., R.S., M.Y., Y.Y., T.A.G., T.T., P.L., H.A., S.W.); and CSIRO Biosciences Program, Parkville, Victoria, Australia (T.P.)
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28
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Bastide MF, Meissner WG, Picconi B, Fasano S, Fernagut PO, Feyder M, Francardo V, Alcacer C, Ding Y, Brambilla R, Fisone G, Jon Stoessl A, Bourdenx M, Engeln M, Navailles S, De Deurwaerdère P, Ko WKD, Simola N, Morelli M, Groc L, Rodriguez MC, Gurevich EV, Quik M, Morari M, Mellone M, Gardoni F, Tronci E, Guehl D, Tison F, Crossman AR, Kang UJ, Steece-Collier K, Fox S, Carta M, Angela Cenci M, Bézard E. Pathophysiology of L-dopa-induced motor and non-motor complications in Parkinson's disease. Prog Neurobiol 2015. [PMID: 26209473 DOI: 10.1016/j.pneurobio.2015.07.002] [Citation(s) in RCA: 343] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Involuntary movements, or dyskinesia, represent a debilitating complication of levodopa (L-dopa) therapy for Parkinson's disease (PD). L-dopa-induced dyskinesia (LID) are ultimately experienced by the vast majority of patients. In addition, psychiatric conditions often manifested as compulsive behaviours, are emerging as a serious problem in the management of L-dopa therapy. The present review attempts to provide an overview of our current understanding of dyskinesia and other L-dopa-induced dysfunctions, a field that dramatically evolved in the past twenty years. In view of the extensive literature on LID, there appeared a critical need to re-frame the concepts, to highlight the most suitable models, to review the central nervous system (CNS) circuitry that may be involved, and to propose a pathophysiological framework was timely and necessary. An updated review to clarify our understanding of LID and other L-dopa-related side effects was therefore timely and necessary. This review should help in the development of novel therapeutic strategies aimed at preventing the generation of dyskinetic symptoms.
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Affiliation(s)
- Matthieu F Bastide
- Univ. de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France; CNRS, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France
| | - Wassilios G Meissner
- Univ. de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France; CNRS, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France; Department of Neurology, University Hospital Bordeaux, France
| | - Barbara Picconi
- Laboratory of Neurophysiology, Fondazione Santa Lucia, IRCCS, Rome, Italy
| | - Stefania Fasano
- Division of Neuroscience, Institute of Experimental Neurology, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Pierre-Olivier Fernagut
- Univ. de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France; CNRS, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France
| | - Michael Feyder
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Veronica Francardo
- Basal Ganglia Pathophysiology Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Cristina Alcacer
- Basal Ganglia Pathophysiology Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Yunmin Ding
- Department of Neurology, Columbia University, New York, USA
| | - Riccardo Brambilla
- Division of Neuroscience, Institute of Experimental Neurology, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Gilberto Fisone
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - A Jon Stoessl
- Pacific Parkinson's Research Centre and National Parkinson Foundation Centre of Excellence, University of British Columbia, Vancouver, Canada
| | - Mathieu Bourdenx
- Univ. de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France; CNRS, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France
| | - Michel Engeln
- Univ. de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France; CNRS, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France
| | - Sylvia Navailles
- Univ. de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France; CNRS, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France
| | - Philippe De Deurwaerdère
- Univ. de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France; CNRS, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France
| | - Wai Kin D Ko
- Univ. de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France; CNRS, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France
| | - Nicola Simola
- Department of Biomedical Sciences, Section of Neuropsychopharmacology, Cagliari University, 09124 Cagliari, Italy
| | - Micaela Morelli
- Department of Biomedical Sciences, Section of Neuropsychopharmacology, Cagliari University, 09124 Cagliari, Italy
| | - Laurent Groc
- Univ. de Bordeaux, Institut Interdisciplinaire de neurosciences, UMR 5297, 33000 Bordeaux, France; CNRS, Institut Interdisciplinaire de neurosciences, UMR 5297, 33000 Bordeaux, France
| | - Maria-Cruz Rodriguez
- Department of Neurology, Hospital Universitario Donostia and Neuroscience Unit, Bio Donostia Research Institute, San Sebastian, Spain
| | - Eugenia V Gurevich
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Maryka Quik
- Center for Health Sciences, SRI International, CA 94025, USA
| | - Michele Morari
- Department of Medical Sciences, Section of Pharmacology, University of Ferrara, Ferrara, Italy
| | - Manuela Mellone
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, 20133 Milano, Italy
| | - Fabrizio Gardoni
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, 20133 Milano, Italy
| | - Elisabetta Tronci
- Department of Biomedical Sciences, Physiology Section, Cagliari University, Cagliari, Italy
| | - Dominique Guehl
- Univ. de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France; CNRS, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France
| | - François Tison
- Univ. de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France; CNRS, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France; Department of Neurology, University Hospital Bordeaux, France
| | | | - Un Jung Kang
- Basal Ganglia Pathophysiology Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Kathy Steece-Collier
- Michigan State University, College of Human Medicine, Department of Translational Science and Molecular Medicine & The Udall Center of Excellence in Parkinson's Disease Research, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Susan Fox
- Morton & Gloria Shulman Movement Disorders Center, Toronto Western Hospital, Toronto, Ontario M4T 2S8, Canada
| | - Manolo Carta
- Department of Biomedical Sciences, Physiology Section, Cagliari University, Cagliari, Italy
| | - M Angela Cenci
- Basal Ganglia Pathophysiology Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Erwan Bézard
- Univ. de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France; CNRS, Institut des Maladies Neurodégénératives, UMR 5293, 33000 Bordeaux, France; Motac Neuroscience Ltd, Manchester, UK.
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29
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Gurevich EV, Gurevich VV. Beyond traditional pharmacology: new tools and approaches. Br J Pharmacol 2015; 172:3229-41. [PMID: 25572005 DOI: 10.1111/bph.13066] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 11/24/2014] [Accepted: 01/02/2015] [Indexed: 12/14/2022] Open
Abstract
Traditional pharmacology is defined as the science that deals with drugs and their actions. While small molecule drugs have clear advantages, there are many cases where they have proved to be ineffective, prone to unacceptable side effects, or where due to a particular disease aetiology they cannot possibly be effective. A dominant feature of the small molecule drugs is their single mindedness: they provide either continuous inhibition or continuous activation of the target. Because of that, these drugs tend to engage compensatory mechanisms leading to drug tolerance, drug resistance or, in some cases, sensitization and consequent loss of therapeutic efficacy over time and/or unwanted side effects. Here we discuss new and emerging therapeutic tools and approaches that have potential for treating the majority of disorders for which small molecules are either failing or cannot be developed. These new tools include biologics, such as recombinant hormones and antibodies, as well as approaches involving gene transfer (gene therapy and genome editing) and the introduction of specially designed self-replicating cells. It is clear that no single method is going to be a 'silver bullet', but collectively, these novel approaches hold promise for curing practically every disorder.
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Affiliation(s)
- E V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - V V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
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DeMille D, Badal BD, Evans JB, Mathis AD, Anderson JF, Grose JH. PAS kinase is activated by direct SNF1-dependent phosphorylation and mediates inhibition of TORC1 through the phosphorylation and activation of Pbp1. Mol Biol Cell 2015; 26:569-82. [PMID: 25428989 PMCID: PMC4310746 DOI: 10.1091/mbc.e14-06-1088] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 10/29/2014] [Accepted: 11/16/2014] [Indexed: 01/22/2023] Open
Abstract
We describe the interplay between three sensory protein kinases in yeast: AMP-regulated kinase (AMPK, or SNF1 in yeast), PAS kinase 1 (Psk1 in yeast), and the target of rapamycin complex 1 (TORC1). This signaling cascade occurs through the SNF1-dependent phosphorylation and activation of Psk1, which phosphorylates and activates poly(A)- binding protein binding protein 1 (Pbp1), which then inhibits TORC1 through sequestration at stress granules. The SNF1-dependent phosphorylation of Psk1 appears to be direct, in that Snf1 is necessary and sufficient for Psk1 activation by alternate carbon sources, is required for altered Psk1 protein mobility, is able to phosphorylate Psk1 in vitro, and binds Psk1 via its substrate-targeting subunit Gal83. Evidence for the direct phosphorylation and activation of Pbp1 by Psk1 is also provided by in vitro and in vivo kinase assays, including the reduction of Pbp1 localization at distinct cytoplasmic foci and subsequent rescue of TORC1 inhibition in PAS kinase-deficient yeast. In support of this signaling cascade, Snf1-deficient cells display increased TORC1 activity, whereas cells containing hyperactive Snf1 display a PAS kinase-dependent decrease in TORC1 activity. This interplay between yeast SNF1, Psk1, and TORC1 allows for proper glucose allocation during nutrient depletion, reducing cell growth and proliferation when energy is low.
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Affiliation(s)
- Desiree DeMille
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602
| | - Bryan D Badal
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602
| | - J Brady Evans
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602
| | - Andrew D Mathis
- Department of Chemistry, Brigham Young University, Provo, UT 84602
| | - Joseph F Anderson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602
| | - Julianne H Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602
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31
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Novel approaches for targeting kinases: allosteric inhibition, allosteric activation and pseudokinases. Future Med Chem 2014; 6:541-61. [PMID: 24649957 DOI: 10.4155/fmc.13.216] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Protein kinases are involved in many essential cellular processes and their deregulation can lead to a variety of diseases, including cancer. The pharmaceutical industry has invested heavily in the identification of kinase inhibitors to modulate these disease-promoting pathways, resulting in several successful drugs. However, the field is challenging as it is difficult to identify novel selective inhibitors with good pharmacokinetic/pharmacodynamic properties. In addition, resistance to kinase inhibitor treatment frequently arises. The identification of non-ATP site targeting ('allosteric') inhibitors, the identification of kinase activators and the expansion of kinase target space to include the less studied members of the family, including atypical- and pseudo-kinases, are potential avenues to overcome these challenges. In this perspective, the opportunities and challenges of following these approaches and others will be discussed.
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32
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Diaz C, Corentin H, Thierry V, Chantal A, Tanguy B, David S, Jean-Marc H, Pascual F, Françoise B, Edgardo F. Virtual screening on an α-helix to β-strand switchable region of the FGFR2 extracellular domain revealed positive and negative modulators. Proteins 2014; 82:2982-97. [PMID: 25082719 DOI: 10.1002/prot.24657] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 06/30/2014] [Accepted: 07/03/2014] [Indexed: 12/15/2022]
Abstract
The secondary structure of some protein segments may vary between α-helix and β-strand. To predict these switchable segments, we have developed an algorithm, Switch-P, based solely on the protein sequence. This algorithm was used on the extracellular parts of FGF receptors. For FGFR2, it predicted that β4 and β5 strands of the third Ig-like domain were highly switchable. These two strands possess a high number of somatic mutations associated with cancer. Analysis of PDB structures of FGF receptors confirmed the switchability prediction for β5. We thus evaluated if compound-driven α-helix/β-strand switching of β5 could modulate FGFR2 signaling. We performed the virtual screening of a library containing 1.4 million of chemical compounds with two models of the third Ig-like domain of FGFR2 showing different secondary structures for β5, and we selected 32 compounds. Experimental testing using proliferation assays with FGF7-stimulated SNU-16 cells and a FGFR2-dependent Erk1/2 phosphorylation assay with FGFR2-transfected L6 cells, revealed activators and inhibitors of FGFR2. Our method for the identification of switchable proteinic regions, associated with our virtual screening approach, provides an opportunity to discover new generation of drugs with under-explored mechanism of action.
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Affiliation(s)
- Constantino Diaz
- Exploratory Unit, Sanofi-Aventis Research and Development, 195 Route d'Espagne, 31036, Toulouse, France
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Unzue A, Dong J, Lafleur K, Zhao H, Frugier E, Caflisch A, Nevado C. Pyrrolo[3,2-b]quinoxaline Derivatives as Types I1/2 and II Eph Tyrosine Kinase Inhibitors: Structure-Based Design, Synthesis, and in Vivo Validation. J Med Chem 2014; 57:6834-44. [DOI: 10.1021/jm5009242] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrea Unzue
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Jing Dong
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Karine Lafleur
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Hongtao Zhao
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Emilie Frugier
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Cristina Nevado
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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Rastelli G, Anighoro A, Chripkova M, Carrassa L, Broggini M. Structure-based discovery of the first allosteric inhibitors of cyclin-dependent kinase 2. Cell Cycle 2014; 13:2296-305. [PMID: 24911186 DOI: 10.4161/cc.29295] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Allosteric targeting of protein kinases via displacement of the structural αC helix with type III allosteric inhibitors is currently gaining a foothold in drug discovery. Recently, the first crystal structure of CDK2 with an open allosteric pocket adjacent to the αC helix has been described, prospecting new opportunities to design more selective inhibitors, but the structure has not yet been exploited for the structure-based design of type III allosteric inhibitors. In this work we report the results of a virtual screening campaign that resulted in the discovery of the first-in-class type III allosteric ligands of CDK2. Using a combination of docking and post-docking analyses made with our tool BEAR, 7 allosteric ligands (hit rate of 20%) with micromolar affinity for CDK2 were identified, some of them inhibiting the growth of breast cancer cell lines in the micromolar range. Competition experiments performed in the presence of the ATP-competitive inhibitor staurosporine confirmed that the 7 ligands are truly allosteric, in agreement with their design. Of these, compound 2 bound CDK2 with an EC50 value of 3 μM and inhibited the proliferation of MDA-MB231 and ZR-75-1 breast cancer cells with IC50 values of approximately 20 μM, while compound 4 had an EC50 value of 71 μM and IC50 values around 4 μM. Remarkably, the most potent compound 4 was able to selectively inhibit CDK2-mediated Retinoblastoma phosphorylation, confirming that its mechanism of action is fully compatible with a selective inhibition of CDK2 phosphorylation in cells. Finally, hit expansion through analog search of the most potent inhibitor 4 revealed an additional ligand 4g with similar in vitro potency on breast cancer cells.
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Affiliation(s)
- Giulio Rastelli
- Life Sciences Department; University of Modena and Reggio Emilia; Modena, Italy
| | - Andrew Anighoro
- Life Sciences Department; University of Modena and Reggio Emilia; Modena, Italy
| | - Martina Chripkova
- IRCCS - Istituto di Ricerche Farmacologiche "Mario Negri"; Milan, Italy
| | - Laura Carrassa
- IRCCS - Istituto di Ricerche Farmacologiche "Mario Negri"; Milan, Italy
| | - Massimo Broggini
- IRCCS - Istituto di Ricerche Farmacologiche "Mario Negri"; Milan, Italy
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Schenone S, Radi M, Musumeci F, Brullo C, Botta M. Biologically Driven Synthesis of Pyrazolo[3,4-d]pyrimidines As Protein Kinase Inhibitors: An Old Scaffold As a New Tool for Medicinal Chemistry and Chemical Biology Studies. Chem Rev 2014; 114:7189-238. [DOI: 10.1021/cr400270z] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Silvia Schenone
- Dipartimento
di Farmacia, Università degli Studi di Genova Viale Benedetto
XV, 3, 16132 Genova, Italy
| | - Marco Radi
- Dipartimento
di Farmacia, Università degli Studi di Parma Viale delle
Scienze, 27/A, 43124 Parma, Italy
| | - Francesca Musumeci
- Dipartimento
di Farmacia, Università degli Studi di Genova Viale Benedetto
XV, 3, 16132 Genova, Italy
| | - Chiara Brullo
- Dipartimento
di Farmacia, Università degli Studi di Genova Viale Benedetto
XV, 3, 16132 Genova, Italy
| | - Maurizio Botta
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena Via Aldo Moro, 2, 53100 Siena, Italy
- Sbarro
Institute for Cancer Research and Molecular Medicine, Center for Biotechnology,
College of Science and Technology, Temple University, BioLife Science
Building, Suite 333, 1900 N 12th Street, Philadelphia, Pennsylvania 19122, United States
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36
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Robertson AJ, Trost B, Scruten E, Robertson T, Mostajeran M, Connor W, Kusalik A, Griebel P, Napper S. Identification of developmentally-specific kinotypes and mechanisms of Varroa mite resistance through whole-organism, kinome analysis of honeybee. Front Genet 2014; 5:139. [PMID: 24904639 PMCID: PMC4033134 DOI: 10.3389/fgene.2014.00139] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 04/28/2014] [Indexed: 01/08/2023] Open
Abstract
Recent investigations associate Varroa destructor (Mesostigmata: Varroidae) parasitism and its associated pathogens and agricultural pesticides with negative effects on colony health, resulting in sporadic global declines in domestic honeybee (Apis mellifera) populations. These events have motivated efforts to develop research tools that can offer insight into the causes of declining bee health as well as identify biomarkers to guide breeding programs. Here we report the development of a bee-specific peptide array for characterizing global cellular kinase activity in whole bee extracts. The arrays reveal distinct, developmentally-specific signaling profiles between bees with differential susceptibility to infestation by Varroa mites. Gene ontology analysis of the differentially phosphorylated peptides indicates that the differential susceptibility to Varroa mite infestation does not reflect compromised immunity; rather, there is evidence for mite-mediated immune suppression within the susceptible phenotype that may reduce the ability of these bees to counter secondary viral infections. This hypothesis is supported by the demonstration of more diverse viral infections in mite-infested, susceptible adult bees. The bee-specific peptide arrays are an effective tool for understanding the molecular basis of this complex phenotype as well as for the discovery and utilization of phosphorylation biomarkers for breeding programs.
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Affiliation(s)
| | - Brett Trost
- Department of Computer Science, University of Saskatchewan Saskatoon, SK, Canada
| | - Erin Scruten
- Vaccine and Infectious Disease Organization, University of Saskatchewan Saskatoon, SK, Canada
| | | | | | - Wayne Connor
- Vaccine and Infectious Disease Organization, University of Saskatchewan Saskatoon, SK, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan Saskatoon, SK, Canada
| | - Philip Griebel
- Vaccine and Infectious Disease Organization, University of Saskatchewan Saskatoon, SK, Canada ; School of Public Health, University of Saskatchewan Saskatoon, SK, Canada
| | - Scott Napper
- Vaccine and Infectious Disease Organization, University of Saskatchewan Saskatoon, SK, Canada ; Department of Biochemistry, University of Saskatchewan Saskatoon, SK, Canada
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37
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DeMille D, Bikman BT, Mathis AD, Prince JT, Mackay JT, Sowa SW, Hall TD, Grose JH. A comprehensive protein-protein interactome for yeast PAS kinase 1 reveals direct inhibition of respiration through the phosphorylation of Cbf1. Mol Biol Cell 2014; 25:2199-215. [PMID: 24850888 PMCID: PMC4091833 DOI: 10.1091/mbc.e13-10-0631] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
PAS kinase is a conserved sensory protein kinase required for glucose homeostasis. The interactome for yeast PAS kinase 1 (Psk1) is identified, revealing 93 binding partners. Evidence is provided for in vivo phosphorylation of Cbf1 and subsequent inhibition of respiration, supporting a role for Psk1 in partitioning glucose for cell growth. Per-Arnt-Sim (PAS) kinase is a sensory protein kinase required for glucose homeostasis in yeast, mice, and humans, yet little is known about the molecular mechanisms of its function. Using both yeast two-hybrid and copurification approaches, we identified the protein–protein interactome for yeast PAS kinase 1 (Psk1), revealing 93 novel putative protein binding partners. Several of the Psk1 binding partners expand the role of PAS kinase in glucose homeostasis, including new pathways involved in mitochondrial metabolism. In addition, the interactome suggests novel roles for PAS kinase in cell growth (gene/protein expression, replication/cell division, and protein modification and degradation), vacuole function, and stress tolerance. In vitro kinase studies using a subset of 25 of these binding partners identified Mot3, Zds1, Utr1, and Cbf1 as substrates. Further evidence is provided for the in vivo phosphorylation of Cbf1 at T211/T212 and for the subsequent inhibition of respiration. This respiratory role of PAS kinase is consistent with the reported hypermetabolism of PAS kinase–deficient mice, identifying a possible molecular mechanism and solidifying the evolutionary importance of PAS kinase in the regulation of glucose homeostasis.
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Affiliation(s)
- Desiree DeMille
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602
| | - Benjamin T Bikman
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602
| | - Andrew D Mathis
- Department of Chemistry, Brigham Young University, Provo, UT 84602
| | - John T Prince
- Department of Chemistry, Brigham Young University, Provo, UT 84602
| | - Jordan T Mackay
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602
| | - Steven W Sowa
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602
| | - Tacie D Hall
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602
| | - Julianne H Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602
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38
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Pharmacological assessment defines Leishmania donovani casein kinase 1 as a drug target and reveals important functions in parasite viability and intracellular infection. Antimicrob Agents Chemother 2013; 58:1501-15. [PMID: 24366737 DOI: 10.1128/aac.02022-13] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Protein kinase inhibitors have emerged as new drugs in various therapeutic areas, including leishmaniasis, an important parasitic disease. Members of the Leishmania casein kinase 1 (CK1) family represent promising therapeutic targets. Leishmania casein kinase 1 isoform 2 (CK1.2) has been identified as an exokinase capable of phosphorylating host proteins, thus exerting a potential immune-suppressive action on infected host cells. Moreover, its inhibition reduces promastigote growth. Despite these important properties, its requirement for intracellular infection and its chemical validation as a therapeutic target in the disease-relevant amastigote stage remain to be established. In this study, we used a multidisciplinary approach combining bioinformatics, biochemical, and pharmacological analyses with a macrophage infection assay to characterize and define Leishmania CK1.2 as a valid drug target. We show that recombinant and transgenic Leishmania CK1.2 (i) can phosphorylate CK1-specific substrates, (ii) is sensitive to temperature, and (iii) is susceptible to CK1-specific inhibitors. CK1.2 is constitutively expressed at both the promastigote insect stage and the vertebrate amastigote stage. We further demonstrated that reduction of CK1 activity by specific inhibitors, such as D4476, blocks promastigote growth, strongly compromises axenic amastigote viability, and decreases the number of intracellular Leishmania donovani and L. amazonensis amastigotes in infected macrophages. These results underline the potential role of CK1 kinases in intracellular survival. The identification of differences in structure and inhibition profiles compared to those of mammalian CK1 kinases opens new opportunities for Leishmania CK1.2 antileishmanial drug development. Our report provides the first chemical validation of Leishmania CK1 protein kinases, required for amastigote intracellular survival, as therapeutic targets.
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CDK/CK1 inhibitors roscovitine and CR8 downregulate amplified MYCN in neuroblastoma cells. Oncogene 2013; 33:5675-87. [PMID: 24317512 DOI: 10.1038/onc.2013.513] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 10/09/2013] [Accepted: 10/21/2013] [Indexed: 12/15/2022]
Abstract
To understand the mechanisms of action of (R)-roscovitine and (S)-CR8, two related pharmacological inhibitors of cyclin-dependent kinases (CDKs), we applied a variety of '-omics' techniques to the human neuroblastoma SH-SY5Y and IMR32 cell lines: (1) kinase interaction assays, (2) affinity competition on immobilized broad-spectrum kinase inhibitors, (3) affinity chromatography on immobilized (R)-roscovitine and (S)-CR8, (4) whole genome transcriptomics analysis and specific quantitative PCR studies, (5) global quantitative proteomics approach and western blot analysis of selected proteins. Altogether, the results show that the major direct targets of these two molecules belong to the CDKs (1,2,5,7,9,12), DYRKs, CLKs and CK1s families. By inhibiting CDK7, CDK9 and CDK12, these inhibitors transiently reduce RNA polymerase 2 activity, which results in downregulation of a large set of genes. Global transcriptomics and proteomics analysis converge to a central role of MYC transcription factors downregulation. Indeed, CDK inhibitors trigger rapid and massive downregulation of MYCN expression in MYCN-amplified neuroblastoma cells as well as in nude mice xenografted IMR32 cells. Inhibition of casein kinase 1 may also contribute to the antitumoral activity of (R)-roscovitine and (S)-CR8. This dual mechanism of action may be crucial in the use of these kinase inhibitors for the treatment of MYC-dependent cancers, in particular neuroblastoma where MYCN amplification is a strong predictor factor for high-risk disease.
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40
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Bruyère C, Meijer L. Targeting cyclin-dependent kinases in anti-neoplastic therapy. Curr Opin Cell Biol 2013; 25:772-9. [PMID: 24011867 DOI: 10.1016/j.ceb.2013.08.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/15/2013] [Accepted: 08/15/2013] [Indexed: 12/12/2022]
Abstract
Cell cycle progression is controlled by sequential activation of cyclin-dependent kinases (CDKs), which are often deregulated in cancer. Consequently numerous pharmacological inhibitors of CDKs have been developed with the aim of treating cancers. The article briefly reviews CDK inhibitors and their use to treat cancers, with specific focus on the use of biomarkers and drugs combination to improve their therapeutic efficacy.
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Affiliation(s)
- Céline Bruyère
- ManRos Therapeutics, Centre de Perharidy, 29680 Roscoff, France
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A novel predicted calcium-regulated kinase family implicated in neurological disorders. PLoS One 2013; 8:e66427. [PMID: 23840464 PMCID: PMC3696010 DOI: 10.1371/journal.pone.0066427] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 05/08/2013] [Indexed: 12/03/2022] Open
Abstract
The catalogues of protein kinases, the essential effectors of cellular signaling, have been charted in Metazoan genomes for a decade now. Yet, surprisingly, using bioinformatics tools, we predicted protein kinase structure for proteins coded by five related human genes and their Metazoan homologues, the FAM69 family. Analysis of three-dimensional structure models and conservation of the classic catalytic motifs of protein kinases present in four out of five human FAM69 proteins suggests they might have retained catalytic phosphotransferase activity. An EF-hand Ca2+-binding domain in FAM69A and FAM69B proteins, inserted within the structure of the kinase domain, suggests they may function as Ca2+-dependent kinases. The FAM69 genes, FAM69A, FAM69B, FAM69C, C3ORF58 (DIA1) and CXORF36 (DIA1R), are by large uncharacterised molecularly, yet linked to several neurological disorders in genetics studies. The C3ORF58 gene is found deleted in autism, and resides in the Golgi. Unusually high cysteine content and presence of signal peptides in some of the family members suggest that FAM69 proteins may be involved in phosphorylation of proteins in the secretory pathway and/or of extracellular proteins.
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Ryšlavá H, Doubnerová V, Kavan D, Vaněk O. Effect of posttranslational modifications on enzyme function and assembly. J Proteomics 2013; 92:80-109. [PMID: 23603109 DOI: 10.1016/j.jprot.2013.03.025] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Revised: 03/01/2013] [Accepted: 03/11/2013] [Indexed: 12/22/2022]
Abstract
The detailed examination of enzyme molecules by mass spectrometry and other techniques continues to identify hundreds of distinct PTMs. Recently, global analyses of enzymes using methods of contemporary proteomics revealed widespread distribution of PTMs on many key enzymes distributed in all cellular compartments. Critically, patterns of multiple enzymatic and nonenzymatic PTMs within a single enzyme are now functionally evaluated providing a holistic picture of a macromolecule interacting with low molecular mass compounds, some of them being substrates, enzyme regulators, or activated precursors for enzymatic and nonenzymatic PTMs. Multiple PTMs within a single enzyme molecule and their mutual interplays are critical for the regulation of catalytic activity. Full understanding of this regulation will require detailed structural investigation of enzymes, their structural analogs, and their complexes. Further, proteomics is now integrated with molecular genetics, transcriptomics, and other areas leading to systems biology strategies. These allow the functional interrogation of complex enzymatic networks in their natural environment. In the future, one might envisage the use of robust high throughput analytical techniques that will be able to detect multiple PTMs on a global scale of individual proteomes from a number of carefully selected cells and cellular compartments. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
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Affiliation(s)
- Helena Ryšlavá
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12840 Prague 2, Czech Republic.
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Mahajan K, Mahajan NP. ACK1 tyrosine kinase: targeted inhibition to block cancer cell proliferation. Cancer Lett 2013; 338:185-92. [PMID: 23597703 DOI: 10.1016/j.canlet.2013.04.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 04/03/2013] [Accepted: 04/08/2013] [Indexed: 01/05/2023]
Abstract
ACK1 tyrosine kinase, located on chromosome 3q29, is aberrantly activated, amplified or mutated in a wide variety of human cancers. While the deregulated kinase is oncogenic and its activation correlates with progression to metastatic stage, its inhibition causes cell cycle arrest, sensitizes cells to ionizing radiation and induces apoptosis. Oncogenicity of ACK1 is not only due to its ability to promote activation of critical pro-survival kinases and harmone receptors by phosphorylating at distinct tyrosine residues, but also by employing a similar mechanism to eliminate a tumor suppressor from cancer cells. Despite the substantial data supporting the oncogenic role of ACK1, and the potential clinical benefit of blocking ACK1 in metastatic disease, to date ACK1-specific small molecule inhibitors have not been exploited for cancer therapy. This review highlights recent advances that elucidate how cancer cells employ ACK1 kinase to their advantage and discusses some of the novel ACK1 inhibitors that have shown promise in pre-clinical studies.
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Affiliation(s)
- Kiran Mahajan
- Drug Discovery Department, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.
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Li H, Redinbo MR, Venkatesh M, Ekins S, Chaudhry A, Bloch N, Negassa A, Mukherjee P, Kalpana G, Mani S. Novel yeast-based strategy unveils antagonist binding regions on the nuclear xenobiotic receptor PXR. J Biol Chem 2013; 288:13655-68. [PMID: 23525103 DOI: 10.1074/jbc.m113.455485] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Ketoconazole binds to and antagonizes pregnane X receptor (PXR) activation. RESULTS Yeast high throughput screens of PXR mutants define a unique region for ketoconazole binding. CONCLUSION Ketoconazole genetically interacts with specific PXR surface residues. SIGNIFICANCE A yeast-based genetic method to discover novel nuclear receptor interactions with ligands that associate with surface binding sites is suggested. The pregnane X receptor (PXR) is a master regulator of xenobiotic metabolism, and its activity is critical toward understanding the pathophysiology of several diseases, including inflammation, cancer, and steatosis. Previous studies have demonstrated that ketoconazole binds to ligand-activated PXR and antagonizes receptor control of gene expression. Structure-function as well as computational docking analysis suggested a putative binding region containing critical charge clamp residues Gln-272, and Phe-264 on the AF-2 surface of PXR. To define the antagonist binding surface(s) of PXR, we developed a novel assay to identify key amino acid residues on PXR based on a yeast two-hybrid screen that examined mutant forms of PXR. This screen identified multiple "gain-of-function" mutants that were "resistant" to the PXR antagonist effects of ketoconazole. We then compared our screen results identifying key PXR residues to those predicted by computational methods. Of 15 potential or putative binding residues based on docking, we identified three residues in the yeast screen that were then systematically verified to functionally interact with ketoconazole using mammalian assays. Among the residues confirmed by our study was Ser-208, which is on the opposite side of the protein from the AF-2 region critical for receptor regulation. The identification of new locations for antagonist binding on the surface or buried in PXR indicates novel aspects to the mechanism of receptor antagonism. These results significantly expand our understanding of antagonist binding sites on the surface of PXR and suggest new avenues to regulate this receptor for clinical applications.
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Affiliation(s)
- Hao Li
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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45
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Cardenas-Aguayo MDC, Kazim SF, Grundke-Iqbal I, Iqbal K. Neurogenic and neurotrophic effects of BDNF peptides in mouse hippocampal primary neuronal cell cultures. PLoS One 2013; 8:e53596. [PMID: 23320097 PMCID: PMC3539976 DOI: 10.1371/journal.pone.0053596] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 11/30/2012] [Indexed: 12/11/2022] Open
Abstract
The level of brain-derived neurotrophic factor (BDNF), a member of the neurotrophin family, is down regulated in Alzheimer’s disease (AD), Parkinson’s disease (PD), depression, stress, and anxiety; conversely the level of this neurotrophin is increased in autism spectrum disorders. Thus, modulating the level of BDNF can be a potential therapeutic approach for nervous system pathologies. In the present study, we designed five different tetra peptides (peptides B-1 to B-5) corresponding to different active regions of BDNF. These tetra peptides were found to be non-toxic, and they induced the expression of neuronal markers in mouse embryonic day 18 (E18) primary hippocampal neuronal cultures. Additionally, peptide B-5 induced the expression of BDNF and its receptor, TrkB, suggesting a positive feedback mechanism. The BDNF peptides induced only a moderate activation (phosphorylation at Tyr 706) of the TrkB receptor, which could be blocked by the Trk’s inhibitor, K252a. Peptide B-3, when combined with BDNF, potentiated the survival effect of this neurotrophin on H2O2-treated E18 hippocampal cells. Peptides B-3 and B-5 were found to work as partial agonists and as partial antagonists competing with BDNF to activate the TrkB receptor in a dose-dependent manner. Taken together, these results suggest that the described BDNF tetra peptides are neurotrophic, can modulate BDNF signaling in a partial agonist/antagonist way, and offer a novel therapeutic approach to neural pathologies where BDNF levels are dysregulated.
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Affiliation(s)
- Maria del Carmen Cardenas-Aguayo
- Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Syed Faraz Kazim
- Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
- Neural and Behavioral Science Graduate Program, State University of New York Downstate Medical Center, Brooklyn, New York, United States of America
| | - Inge Grundke-Iqbal
- Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
| | - Khalid Iqbal
- Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, United States of America
- * E-mail:
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46
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Druggability predictions: methods, limitations, and applications. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1134] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Tahtouh T, Elkins JM, Filippakopoulos P, Soundararajan M, Burgy G, Durieu E, Cochet C, Schmid RS, Lo DC, Delhommel F, Oberholzer AE, Pearl LH, Carreaux F, Bazureau JP, Knapp S, Meijer L. Selectivity, cocrystal structures, and neuroprotective properties of leucettines, a family of protein kinase inhibitors derived from the marine sponge alkaloid leucettamine B. J Med Chem 2012; 55:9312-30. [PMID: 22998443 DOI: 10.1021/jm301034u] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DYRKs (dual specificity, tyrosine phosphorylation regulated kinases) and CLKs (cdc2-like kinases) are implicated in the onset and development of Alzheimer's disease and Down syndrome. The marine sponge alkaloid leucettamine B was recently identified as an inhibitor of DYRKs/CLKs. Synthesis of analogues (leucettines) led to an optimized product, leucettine L41. Leucettines were cocrystallized with DYRK1A, DYRK2, CLK3, PIM1, and GSK-3β. The selectivity of L41 was studied by activity and interaction assays of recombinant kinases and affinity chromatography and competition affinity assays. These approaches revealed unexpected potential secondary targets such as CK2, SLK, and the lipid kinase PIKfyve/Vac14/Fig4. L41 displayed neuroprotective effects on glutamate-induced HT22 cell death. L41 also reduced amyloid precursor protein-induced cell death in cultured rat brain slices. The unusual multitarget selectivity of leucettines may account for their neuroprotective effects. This family of kinase inhibitors deserves further optimization as potential therapeutics against neurodegenerative diseases such as Alzheimer's disease.
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Affiliation(s)
- Tania Tahtouh
- CNRS, "Protein Phosphorylation & Human Disease" Group, Station Biologique, 29680 Roscoff, Bretagne, France
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48
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Yeo WK, Go ML, Nilar S. Extraction and validation of substructure profiles for enriching compound libraries. J Comput Aided Mol Des 2012; 26:1127-41. [PMID: 22983491 DOI: 10.1007/s10822-012-9604-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 09/07/2012] [Indexed: 11/26/2022]
Abstract
Compounds known to be potent against a specific protein target may potentially contain a signature profile of common substructures that is highly correlated to their potency. These substructure profiles may be useful in enriching compound libraries or for prioritizing compounds against a specific protein target. With this objective in mind, a set of compounds with known potency against six selected kinases (2 each from 3 kinase families) was used to generate binary molecular fingerprints. Each fingerprint key represents a substructure that is found within a compound and the frequency with which the fingerprint occurs was then tabulated. Thereafter, a frequent pattern mining technique was applied with the aim of uncovering substructures that are not only well represented among known potent inhibitors but are also unrepresented among known inactive compounds and vice versa. Substructure profiles that are representative of potent inhibitors against each of the 3 kinase families were thus extracted. Based on our validation results, these substructure profiles demonstrated significant enrichment for highly potent compounds against their respective kinase targets. The advantages of using our approach over conventional methods in analyzing such datasets and its application in the mining of substructures for enriching compound libraries are presented.
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Affiliation(s)
- Wee Kiang Yeo
- Novartis Institute for Tropical Diseases, Chromos, Singapore, Singapore.
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Laine É, Martínez L, Ladant D, Malliavin T, Blondel A. Molecular motions as a drug target: mechanistic simulations of anthrax toxin edema factor function led to the discovery of novel allosteric inhibitors. Toxins (Basel) 2012; 4:580-604. [PMID: 23012649 PMCID: PMC3446745 DOI: 10.3390/toxins4080580] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 07/04/2012] [Accepted: 07/18/2012] [Indexed: 01/14/2023] Open
Abstract
Edema Factor (EF) is a component of Bacillus anthracis toxin essential for virulence. Its adenylyl cyclase activity is induced by complexation with the ubiquitous eukaryotic cellular protein, calmodulin (CaM). EF and its complexes with CaM, nucleotides and/or ions, have been extensively characterized by X-ray crystallography. Those structural data allowed molecular simulations analysis of various aspects of EF action mechanism, including the delineation of EF and CaM domains through their association energetics, the impact of calcium binding on CaM, and the role of catalytic site ions. Furthermore, a transition path connecting the free inactive form to the CaM-complexed active form of EF was built to model the activation mechanism in an attempt to define an inhibition strategy. The cavities at the surface of EF were determined for each path intermediate to identify potential sites where the binding of a ligand could block activation. A non-catalytic cavity (allosteric) was found to shrink rapidly at early stages of the path and was chosen to perform virtual screening. Amongst 18 compounds selected in silico and tested in an enzymatic assay, 6 thiophen ureidoacid derivatives formed a new family of EF allosteric inhibitors with IC50 as low as 2 micromolars.
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Affiliation(s)
- Élodie Laine
- Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, 61, avenue du Président Wilson, 94235 Cachan cedex, France;
| | - Leandro Martínez
- The Molecular Biotechnology Group, Institute of Physics of São Carlos, University of São Paulo, Av. Trabalhador Sãocarlense, 400, 13566-590 São Carlos, SP, Brazil;
| | - Daniel Ladant
- Unité de Biochimie des Interactions Macromoléculaires and CNRS UMR 3528, Département de Biologie Structurale et Chimie, Institut Pasteur, 28, rue du Dr. Roux, 75724 Paris Cedex 15, France;
| | - Thérèse Malliavin
- Unité de Bioinformatique Structurale and CNRS UMR 3528, Département de Biologie Structurale et Chimie, Institut Pasteur, 25, rue du Dr. Roux, 75724 Paris Cedex 15, France;
| | - Arnaud Blondel
- Unité de Bioinformatique Structurale and CNRS UMR 3528, Département de Biologie Structurale et Chimie, Institut Pasteur, 25, rue du Dr. Roux, 75724 Paris Cedex 15, France;
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50
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Getlik M, Simard JR, Termathe M, Grütter C, Rabiller M, van Otterlo WAL, Rauh D. Fluorophore labeled kinase detects ligands that bind within the MAPK insert of p38α kinase. PLoS One 2012; 7:e39713. [PMID: 22768308 PMCID: PMC3388095 DOI: 10.1371/journal.pone.0039713] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 05/25/2012] [Indexed: 11/19/2022] Open
Abstract
The vast majority of small molecules known to modulate kinase activity, target the highly conserved ATP-pocket. Consequently, such ligands are often less specific and in case of inhibitors, this leads to the inhibition of multiple kinases. Thus, selective modulation of kinase function remains a major hurdle. One of the next great challenges in kinase research is the identification of ligands which bind to less conserved sites and target the non-catalytic functions of protein kinases. However, approaches that allow for the unambiguous identification of molecules that bind to these less conserved sites are few in number. We have previously reported the use of fluorescent labels in kinases (FLiK) to develop direct kinase binding assays that exclusively detect ligands which stabilize inactive (DFG-out) kinase conformations. Here, we present the successful application of the FLiK approach to develop a high-throughput binding assay capable of directly monitoring ligand binding to a remote site within the MAPK insert of p38α mitogen-activated protein kinase (MAPK). Guided by the crystal structure of an initially identified hit molecule in complex with p38α, we developed a tight binding ligand which may serve as an ideal starting point for further investigations of the biological function of the MAPK insert in regulating the p38α signaling pathway.
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Affiliation(s)
- Matthäus Getlik
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Jeffrey R. Simard
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Martin Termathe
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Christian Grütter
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
- Fakultät Chemie, Chemische Biologie, Technische Universität Dortmund, Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Matthias Rabiller
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Willem A. L. van Otterlo
- Department of Chemistry and Polymer Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Daniel Rauh
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
- Fakultät Chemie, Chemische Biologie, Technische Universität Dortmund, Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
- * E-mail:
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