1
|
Eserci H, Çetin M, Aydınoğlu F, Eçik ET, Okutan E. Naphthalimide-BODIPY dyads: Synthesis, characterization, photophysical properties, live cell imaging and antimicrobial effect. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
2
|
Abstract
Fluorescent dyes attached to kinase inhibitors (KIs) can be used to probe kinases in vitro, in cells, and in vivo. Ideal characteristics of the dyes vary with their intended applications. Fluorophores used in vitro may inform on kinase active site environments, hence the dyes used should be small and have minimal impact on modes of binding. These probes may have short wavelength emissions since blue fluorophores are perfectly adequate in this context. Thus, for instance, KI fragments that mimic nucleobases may be modified to be fluorescent with minimal perturbation to the kinase inhibitor structure. However, progressively larger dyes, that emit at longer wavelengths, are required for cellular and in vivo work. In cells, it is necessary to have emissions above autofluorescence of biomolecules, and near infrared dyes are needed to enable excitation and observation through tissue in vivo. This review is organized to describe probes intended for applications in vitro, in cells, then in vivo. The readers will observe that the probes featured tend to become larger and responsive to the near infared end of the spectrum as the review progresses. Readers may also be surprised to realize that relatively few dyes have been used for fluorophore-kinase inhibitor conjugates, and the area is open for innovations in the types of fluorophores used.
Collapse
Affiliation(s)
- Syed Muhammad Usama
- Department of Chemistry, Texas A&M University, Box 30012, College Station, TX 77842, USA.
| | | | | |
Collapse
|
3
|
Laurin CMC, Bluck JP, Chan AKN, Keller M, Boczek A, Scorah AR, See KFL, Jennings LE, Hewings DS, Woodhouse F, Reynolds JK, Schiedel M, Humphreys PG, Biggin PC, Conway SJ. Fragment-Based Identification of Ligands for Bromodomain-Containing Factor 3 of Trypanosoma cruzi. ACS Infect Dis 2021; 7:2238-2249. [PMID: 33203208 DOI: 10.1021/acsinfecdis.0c00618] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Trypanosoma cruzi (T. cruzi) parasite is the cause of Chagas disease, a neglected disease endemic in South America. The life cycle of the T. cruzi parasite is complex and includes transitions between distinct life stages. This change in phenotype (without a change in genotype) could be controlled by epigenetic regulation, and might involve the bromodomain-containing factors 1-5 (TcBDF1-5). However, little is known about the function of the TcBDF1-5. Here we describe a fragment-based approach to identify ligands for T. cruzi bromodomain-containing factor 3 (TcBDF3). We expressed a soluble construct of TcBDF3 in E. coli, and used this to develop a range of biophysical assays for this protein. Fragment screening identified 12 compounds that bind to the TcBDF3 bromodomain. On the basis of this screen, we developed functional ligands containing a fluorescence or 19F reporter group, and a photo-crosslinking probe for TcBDF3. These tool compounds will be invaluable in future studies on the function of TcBDF3 and will provide insight into the biology of T. cruzi.
Collapse
Affiliation(s)
- Corentine M. C. Laurin
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Joseph P. Bluck
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
- Department of Biochemistry, University of Oxford, 3 Parks Road, Oxford OX1 3QU, UK
| | - Anthony K. N. Chan
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Michelle Keller
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Andrew Boczek
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Amy R. Scorah
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - K. F. Larissa See
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Laura E. Jennings
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - David S. Hewings
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Fern Woodhouse
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Jessica K. Reynolds
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Matthias Schiedel
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | | | - Philip C. Biggin
- Department of Biochemistry, University of Oxford, 3 Parks Road, Oxford OX1 3QU, UK
| | - Stuart J. Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| |
Collapse
|
4
|
Tsuji K, Hymel D, Burke TR. A new genre of fluorescence recovery assay to evaluate polo-like kinase 1 ATP-competitive inhibitors. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:4418-4421. [PMID: 32970049 PMCID: PMC7523589 DOI: 10.1039/d0ay01223h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Using a probe consisting of a fluorescein-labeled variant of the potent polo-like kinase 1 (Plk1) inhibitor BI2536 [FITC-PEG-Lys(BI2536) 4], we were able to determine half maximal inhibitory concentration (IC50) of ATP-competitive Type 1 inhibitors of Plk1 by means of a fluorescence recovery assay. This methodology represents a cost-effective and simple alternative to traditional kinase assays for initial screening of potential Plk1 inhibitors.
Collapse
Affiliation(s)
- Kohei Tsuji
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, 21702 USA.
| | | | | |
Collapse
|
5
|
Liu S, Yosief HO, Dai L, Huang H, Dhawan G, Zhang X, Muthengi AM, Roberts J, Buckley DL, Perry JA, Wu L, Bradner JE, Qi J, Zhang W. Structure-Guided Design and Development of Potent and Selective Dual Bromodomain 4 (BRD4)/Polo-like Kinase 1 (PLK1) Inhibitors. J Med Chem 2018; 61:7785-7795. [PMID: 30125504 PMCID: PMC6309379 DOI: 10.1021/acs.jmedchem.8b00765] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The simultaneous inhibition of polo-like kinase 1 (PLK1) and BRD4 bromodomain by a single molecule could lead to the development of an effective therapeutic strategy for a variety of diseases in which PLK1 and BRD4 are implicated. Compound 23 has been found to be a potent dual kinase-bromodomain inhibitor (BRD4-BD1 IC50 = 28 nM, PLK1 IC50 = 40 nM). Compound 6 was found to be the most selective PLK1 inhibitor over BRD4 in our series (BRD4-BD1 IC50 = 2579 nM, PLK1 IC50 = 9.9 nM). Molecular docking studies with 23 and BRD4-BD1/PLK1 as well as with 6 corroborate the biochemical assay results.
Collapse
Affiliation(s)
- Shuai Liu
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
| | - Hailemichael O Yosief
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
| | - Lingling Dai
- Phase I Clinical Trial Center & Department of Clinical Pharmacology, Xiangya Hospital , Central South University , Changsha , Hunan 410008 , P.R. China
| | - He Huang
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794-3400 , United States
| | - Gagan Dhawan
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
- Department of Biomedical Science, Acharya Narendra Dev College , University of Delhi , New Delhi 110019 , India
| | - Xiaofeng Zhang
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
| | - Alex M Muthengi
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
| | | | | | | | | | - James E Bradner
- Novartis Institutes for Biomedical Research , Cambridge , Massachusetts 02139 , United States
| | - Jun Qi
- Department of Medicine , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Wei Zhang
- Department of Chemistry , University of Massachusetts-Boston , Boston , Massachusetts 02125 , United States
| |
Collapse
|
6
|
Dissection of Protein Kinase Pathways in Live Cells Using Photoluminescent Probes: Surveillance or Interrogation? CHEMOSENSORS 2018. [DOI: 10.3390/chemosensors6020019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
7
|
Saarbach J, Lindberg E, Folliet S, Georgeon S, Hantschel O, Winssinger N. Kinase-templated abiotic reaction. Chem Sci 2017; 8:5119-5125. [PMID: 28970898 PMCID: PMC5615226 DOI: 10.1039/c7sc01416c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/20/2017] [Indexed: 12/16/2022] Open
Abstract
Protein kinases are quintessential regulators of cellular function. Numerous pathologies are intimately linked to the dysregulated activity of a particular protein kinase. Herein we report a technology based on a proximity-induced chemical transformation that enables the detection and imaging of specific kinases. Using two probes that target the nucleotide-binding site and substrate binding site of a target kinase respectively, the reagents appended on the probes are brought within reactive distance thereby enabling the chemical transformation. The reaction used for sensing is a ruthenium-photocatalyzed reduction of a pyridinium immolative linker, which uncages a fluorophore (rhodamine). We demonstrate that this technology can be used to discriminate between closely related kinases with a high signal to noise ratio. We further demonstrate that the technology operates within the complexity of a cellular context with a good correlation between the level of kinase activity and fluorescence output.
Collapse
Affiliation(s)
- J Saarbach
- Faculty of Science , Department of Organic Chemistry , NCCR Chemical Biology , University of Geneva , 30 quai Ernest Ansermet , Geneva , Switzerland .
| | - E Lindberg
- Faculty of Science , Department of Organic Chemistry , NCCR Chemical Biology , University of Geneva , 30 quai Ernest Ansermet , Geneva , Switzerland .
| | - S Folliet
- Faculty of Science , Department of Organic Chemistry , NCCR Chemical Biology , University of Geneva , 30 quai Ernest Ansermet , Geneva , Switzerland .
| | - S Georgeon
- Swiss Institute for Experimental Cancer Research (ISREC) , NCCR Chemical Biology , School of Life Sciences , École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - O Hantschel
- Swiss Institute for Experimental Cancer Research (ISREC) , NCCR Chemical Biology , School of Life Sciences , École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - N Winssinger
- Faculty of Science , Department of Organic Chemistry , NCCR Chemical Biology , University of Geneva , 30 quai Ernest Ansermet , Geneva , Switzerland .
| |
Collapse
|
8
|
Ayoub AM, Hawk LML, Herzig RJ, Jiang J, Wisniewski AJ, Gee CT, Zhao P, Zhu JY, Berndt N, Offei-Addo NK, Scott TG, Qi J, Bradner JE, Ward TR, Schönbrunn E, Georg GI, Pomerantz WC. BET Bromodomain Inhibitors with One-Step Synthesis Discovered from Virtual Screen. J Med Chem 2017; 60:4805-4817. [PMID: 28535045 PMCID: PMC5558211 DOI: 10.1021/acs.jmedchem.6b01336] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Chemical inhibition of epigenetic regulatory proteins BrdT and Brd4 is emerging as a promising therapeutic strategy in contraception, cancer, and heart disease. We report an easily synthesized dihydropyridopyrimidine pan-BET inhibitor scaffold, which was uncovered via a virtual screen followed by testing in a fluorescence anisotropy assay. Dihydropyridopyimidine 3 was subjected to further characterization and is highly selective for the BET family of bromodomains. Structure-activity relationship data and ligand deconstruction highlight the importance of the substitution of the uracil moiety for potency and selectivity. Compound 3 was also cocrystallized with Brd4 for determining the ligand binding pose and rationalizing subsequent structure-activity data. An additional series of dihydropyridopyrimidines was synthesized to exploit the proximity of a channel near the ZA loop of Brd4, leading to compounds with submicromolar affinity and cellular target engagement. Given these findings, novel and easily synthesized inhibitors are being introduced to the growing field of bromodomain inhibitor development.
Collapse
Affiliation(s)
- Alex M. Ayoub
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States
| | - Laura M. L. Hawk
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States
| | - Ryan J. Herzig
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN 55455, United States
| | - Jiewei Jiang
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN 55455, United States
| | - Andrea J. Wisniewski
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN 55455, United States
| | - Clifford T. Gee
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States
| | - Peiliang Zhao
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN 55455, United States
| | - Jin-Yi Zhu
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Norbert Berndt
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Nana K. Offei-Addo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 360 Longwood Avenue, Boston, MA, 02215, United States
| | - Thomas G. Scott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 360 Longwood Avenue, Boston, MA, 02215, United States
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 360 Longwood Avenue, Boston, MA, 02215, United States
| | - James E. Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 360 Longwood Avenue, Boston, MA, 02215, United States
| | - Timothy R. Ward
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN 55455, United States
| | - Ernst Schönbrunn
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, United States
| | - Gunda I. Georg
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN 55455, United States
| | - William C.K. Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States
| |
Collapse
|
9
|
Rausch K, Hackett BA, Weinbren NL, Reeder SM, Sadovsky Y, Hunter CA, Schultz DC, Coyne CB, Cherry S. Screening Bioactives Reveals Nanchangmycin as a Broad Spectrum Antiviral Active against Zika Virus. Cell Rep 2017; 18:804-815. [PMID: 28099856 PMCID: PMC5270376 DOI: 10.1016/j.celrep.2016.12.068] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/07/2016] [Accepted: 12/20/2016] [Indexed: 12/20/2022] Open
Abstract
Zika virus is an emerging arthropod-borne flavivirus for which there are no vaccines or specific therapeutics. We screened a library of 2,000 bioactive compounds for their ability to block Zika virus infection in three distinct cell types with two different strains of Zika virus. Using a microscopy-based assay, we validated 38 drugs that inhibited Zika virus infection, including FDA-approved nucleoside analogs. Cells expressing high levels of the attachment factor AXL can be protected from infection with receptor tyrosine kinase inhibitors, while placental-derived cells that lack AXL expression are insensitive to this inhibition. Importantly, we identified nanchangmycin as a potent inhibitor of Zika virus entry across all cell types tested, including physiologically relevant primary cells. Nanchangmycin also was active against other medically relevant viruses, including West Nile, dengue, and chikungunya viruses that use a similar route of entry. This study provides a resource of small molecules to study Zika virus pathogenesis.
Collapse
Affiliation(s)
- Keiko Rausch
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Brent A Hackett
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathan L Weinbren
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sophia M Reeder
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yoel Sadovsky
- Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA 19104, USA; Department of Obstetrics, Gynecology, and Reproductive Science, University of Pittsburgh, Pittsburgh, PA 19104, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 19104, USA
| | - Christopher A Hunter
- Department of Pathobiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David C Schultz
- High-Throughput Screening Core, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Carolyn B Coyne
- Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA 19104, USA; Department of Obstetrics, Gynecology, and Reproductive Science, University of Pittsburgh, Pittsburgh, PA 19104, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 19104, USA
| | - Sara Cherry
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
10
|
Urick AK, Calle LP, Espinosa JF, Hu H, Pomerantz WCK. Protein-Observed Fluorine NMR Is a Complementary Ligand Discovery Method to 1H CPMG Ligand-Observed NMR. ACS Chem Biol 2016; 11:3154-3164. [PMID: 27627661 PMCID: PMC8325173 DOI: 10.1021/acschembio.6b00730] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
To evaluate its potential as a ligand discovery tool, we compare a newly developed 1D protein-observed fluorine NMR (PrOF NMR) screening method with the well-characterized ligand-observed 1H CPMG NMR screen. We selected the first bromodomain of Brd4 as a model system to benchmark PrOF NMR because of the high ligandability of Brd4 and the need for small molecule inhibitors of related epigenetic regulatory proteins. We compare the two methods' hit sensitivity, triaging ability, experiment speed, material consumption, and the potential for false positives and negatives. To this end, we screened 930 fragment molecules against Brd4 in mixtures of five and followed up these studies with mixture deconvolution and affinity characterization of the top hits. In selected examples, we also compare the environmental responsiveness of the 19F chemical shift to 1H in 1D-protein observed 1H NMR experiments. To address concerns of perturbations from fluorine incorporation, ligand binding trends and affinities were verified via thermal shift assays and isothermal titration calorimetry. We conclude that for the protein understudy here, PrOF NMR and 1H CPMG have similar sensitivity, with both being effective tools for ligand discovery. In cases where an unlabeled protein can be used, 1D protein-observed 1H NMR may also be effective; however, the 19F chemical shift remains significantly more responsive.
Collapse
Affiliation(s)
- Andrew K. Urick
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Luis Pablo Calle
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Centro de Investigación Lilly, 28108 Alcobendas, Madrid, Spain
| | - Juan F. Espinosa
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Centro de Investigación Lilly, 28108 Alcobendas, Madrid, Spain
| | - Haitao Hu
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - William C. K. Pomerantz
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
11
|
Hawk LML, Gee CT, Urick AK, Hu H, Pomerantz WCK. Paramagnetic relaxation enhancement for protein-observed 19F NMR as an enabling approach for efficient fragment screening. RSC Adv 2016; 6:95715-95721. [PMID: 28496971 PMCID: PMC5421645 DOI: 10.1039/c6ra21226c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Protein-observed 19F (PrOF) NMR is an emerging tool for ligand discovery. To optimize the efficiency of PrOF NMR experiments, paramagnetic relaxation enhancement through the addition of chelated Ni(II) was used to shorten longitudinal relaxation time without causing significant line broadening. Thus enhancing relaxation time leads to shorter experiments without perturbing the binding of low- or high-affinity ligands. This method allows for time-efficient screening of potential ligands for a wide variety of proteins in the growing field of fragment-based ligand discovery.
Collapse
Affiliation(s)
- Laura M L Hawk
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States
| | - Clifford T Gee
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States
| | - Andrew K Urick
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, United States
| | - Haitao Hu
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, United States
| |
Collapse
|
12
|
Neena KK, Thilagar P. Conformational Restrictions in meso
-(2-Thiazolyl)-BODIPYs: Large Stokes Shift and pH-Dependent Optical Properties. Chempluschem 2016; 81:955-963. [DOI: 10.1002/cplu.201600254] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/21/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Kalluvettukuzhy K. Neena
- Department of Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore 560012 India
| | - Pakkirisamy Thilagar
- Department of Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore 560012 India
| |
Collapse
|
13
|
Leriche G, Chen AC, Kim S, Selkoe DJ, Yang J. Fluorescent Analogue of Batimastat Enables Imaging of α-Secretase in Living Cells. ACS Chem Neurosci 2016; 7:40-5. [PMID: 26559179 DOI: 10.1021/acschemneuro.5b00283] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The ADAM family of metalloproteases cleave a diverse range of transmembrane substrates, resulting in the release of their soluble ectodomains. This process of protein shedding, termed α-secretase processing, is involved in many facets of both normal and disease related cellular function. While the processing of substrates has been well documented, the regulation and trafficking of the ADAMs are less well understood. Tools that allow for the study of ADAMs under their native environment will allow for a better understanding of their regulation and activity. Here we describe the design and evaluation of a novel fluorescent analogue of a well-characterized ADAM inhibitor, Batimastat. This probe exhibited similar activity for inhibiting α-secretase processing in cells as did Batimastat. Importantly, this probe specifically labeled ADAMs fluorescently in both fixed and living cells, enabling the possibility to study the trafficking of α-secretase proteins in a dynamic environment.
Collapse
Affiliation(s)
- Geoffray Leriche
- Department
of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, United States
| | - Allen C. Chen
- Ann
Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Sumin Kim
- Ann
Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Dennis J. Selkoe
- Ann
Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jerry Yang
- Department
of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, United States
| |
Collapse
|
14
|
Urick AK, Hawk LML, Cassel MK, Mishra NK, Liu S, Adhikari N, Zhang W, dos Santos CO, Hall JL, Pomerantz WCK. Dual Screening of BPTF and Brd4 Using Protein-Observed Fluorine NMR Uncovers New Bromodomain Probe Molecules. ACS Chem Biol 2015; 10:2246-56. [PMID: 26158404 PMCID: PMC4858447 DOI: 10.1021/acschembio.5b00483] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bromodomain-containing protein dysregulation is linked to cancer, diabetes, and inflammation. Selective inhibition of bromodomain function is a newly proposed therapeutic strategy. We describe a (19)F NMR dual screening method for small molecule discovery using fluorinated tryptophan resonances on two bromodomain-containing proteins. The chemical shift dispersion of (19)F resonances within fluorine-labeled proteins enables the simultaneous analysis of two fluorinated bromodomains by NMR. A library of 229 small molecules was screened against the first bromodomain of Brd4 and the BPTF bromodomain. We report the first small molecule selective for BPTF over Brd4, termed AU1. The Kd = 2.8 μM for AU1, which is active in a cell-based reporter assay. No binding is detected with Brd4. Three new Brd4 inhibitors with submicromolar affinity were also discovered. Brd4 hits were validated in a thermal stability assay and potency determined via fluorescence anisotropy. The speed, ease of interpretation, and low protein concentration needed for protein-observed (19)F NMR experiments in a multiprotein format offers a new method to discover and characterize selective ligands for bromodomain-containing proteins.
Collapse
Affiliation(s)
- Andrew K. Urick
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE Minneapolis, MN 55455
| | - Laura M. L. Hawk
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE Minneapolis, MN 55455
| | - Melissa K. Cassel
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE Minneapolis, MN 55455
| | - Neeraj K. Mishra
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE Minneapolis, MN 55455
| | - Shuai Liu
- Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA 02125
| | - Neeta Adhikari
- Lillehei Heart Institute, Department of Medicine, 2231 6thStreet SE, Minneapolis, MN 55455
| | - Wei Zhang
- Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA 02125
| | | | - Jennifer L. Hall
- Lillehei Heart Institute, Department of Medicine, 2231 6thStreet SE, Minneapolis, MN 55455
| | | |
Collapse
|
15
|
Ekebergh A, Lingblom C, Sandin P, Wennerås C, Mårtensson J. Exploring a cascade Heck-Suzuki reaction based route to kinase inhibitors using design of experiments. Org Biomol Chem 2015; 13:3382-92. [PMID: 25658776 DOI: 10.1039/c4ob02694b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Design of Experiments (DoE) has been used to optimize a diversity oriented palladium catalyzed cascade Heck-Suzuki reaction for the construction of 3-alkenyl substituted cyclopenta[b]indole compounds. The obtained DoE model revealed a reaction highly dependent on the ligand. Guided by the model, an optimal ligand was chosen that selectively delivered the desired products in high yields. The conditions were applicable with a variety of boronic acids and were used to synthesize a library of 3-alkenyl derivatized compounds. Focusing on inhibition of kinases relevant for combating melanoma, the library was used in an initial structure-activity survey. In line with the observed kinase inhibition, cellular studies revealed one of the more promising derivatives to inhibit cell proliferation via an apoptotic mechanism.
Collapse
Affiliation(s)
- Andreas Ekebergh
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.
| | | | | | | | | |
Collapse
|
16
|
Mukherjee S, Thilagar P. Fine-Tuning Dual Emission and Aggregation-Induced Emission Switching in NPI-BODIPY Dyads. Chemistry 2014; 20:9052-62. [DOI: 10.1002/chem.201305049] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Indexed: 11/08/2022]
|
17
|
Vetter ML, Zhang Z, Liu S, Wang J, Cho H, Zhang J, Zhang W, Gray NS, Yang PL. Fluorescent visualization of Src by using dasatinib-BODIPY. Chembiochem 2014; 15:1317-24. [PMID: 24828915 DOI: 10.1002/cbic.201402010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Indexed: 12/12/2022]
Abstract
Many biological experiments are not compatible with the use of immunofluorescence, genetically encoded fluorescent tags, or FRET-based reporters. Conjugation of existing kinase inhibitors to cell-permeable fluorophores can provide a generalized approach to develop fluorescent probes of intracellular kinases. Here, we report the development of a small molecule probe of Src through conjugation of BODIPY to two well-established dual Src-Abl kinase inhibitors, dasatinib and saracatinib. We show that this approach is not successful for saracatinib but that dasatinib-BODIPY largely retains the biological activity of its parent compound and can be used to monitor the presence of Src kinase in individual cells by flow cytometry. It can also be used to track the localization of Src by fixed and live-cell fluorescence microscopy. This strategy could enable generation of additional kinase-specific probes useful in systems not amenable to genetic manipulation or could be used together with fluorescent proteins to enable a multiplexed assay readout.
Collapse
Affiliation(s)
- Michael L Vetter
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115 (USA)
| | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Ogunleye LO, Jester BW, Riemen AJ, Badran AH, Wang P, Ghosh I. When tight is too tight: Dasatinib and its lower affinity analogue for profiling kinase inhibitors in a three-hybrid split-luciferase system. MEDCHEMCOMM 2014. [DOI: 10.1039/c3md00275f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report new CIDs based on Dasatinib and its analogues for profiling kinase inhibitors using a split-luciferase screen.
Collapse
Affiliation(s)
- Luca O. Ogunleye
- University of Arizona
- Department of Chemistry and Biochemistry
- Tucson
- USA
| | | | | | - Ahmed H. Badran
- University of Arizona
- Department of Chemistry and Biochemistry
- Tucson
- USA
| | - Ping Wang
- University of Arizona
- Department of Chemistry and Biochemistry
- Tucson
- USA
| | - Indraneel Ghosh
- University of Arizona
- Department of Chemistry and Biochemistry
- Tucson
- USA
| |
Collapse
|
19
|
Wang L, Wang JW, Cui AJ, Cai XX, Wan Y, Chen Q, He MY, Zhang W. Regioselective 2,6-dihalogenation of BODIPYs in 1,1,1,3,3,3-hexafluoro-2-propanol and preparation of novel meso-alkyl polymeric BODIPY dyes. RSC Adv 2013. [DOI: 10.1039/c3ra41298a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
20
|
Zambaldo C, Sadhu KK, Karthikeyan G, Barluenga S, Daguer JP, Winssinger N. Selective affinity-based probe for oncogenic kinases suitable for live cell imaging. Chem Sci 2013. [DOI: 10.1039/c3sc21856b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
|