251
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Tomohara K, Ito T, Onikata S, Kato A, Adachi I. Discovery of hyaluronidase inhibitors from natural products and their mechanistic characterization under DMSO-perturbed assay conditions. Bioorg Med Chem Lett 2017; 27:1620-1623. [PMID: 28202328 DOI: 10.1016/j.bmcl.2017.01.083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 01/24/2017] [Accepted: 01/27/2017] [Indexed: 12/19/2022]
Abstract
The present study discovered four novel hyaluronan-degrading enzyme (hyaluronidase) inhibitors including chikusetsusaponins and catechins through the activity-guided separation of Panax japonicus and Prunus salicina, respectively. Although the discovery resulted in identification of usual frequent hitters, subsequent mechanistic characterizations under our DMSO-perturbed assay conditions and related protocols revealed that chikusetusaponin IV would serve as an aggregating and non-specific binding inhibitor, while (-)-epicatechin would interact specifically with enzyme at the catalytic site or more likely at a kind of catechin-binding site with a relatively week inhibitory activity. The latter description might provide a possible explanation for the well-known fact that a series of catechin have been described as frequent hitters in biological assays with a moderate activity. Thus, the present study demonstrated a practical and robust methodology to characterize initial screening hits mechanistically molecule-by-molecule in the early stage of natural product-based drug discovery.
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Affiliation(s)
- Keisuke Tomohara
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
| | - Tomohiro Ito
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Saika Onikata
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Atsushi Kato
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Isao Adachi
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
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252
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Duan D, Torosyan H, Elnatan D, McLaughlin CK, Logie J, Shoichet MS, Agard DA, Shoichet BK. Internal Structure and Preferential Protein Binding of Colloidal Aggregates. ACS Chem Biol 2017; 12:282-290. [PMID: 27983786 DOI: 10.1021/acschembio.6b00791] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Colloidal aggregates of small molecules are the most common artifact in early drug discovery, sequestering and inhibiting target proteins without specificity. Understanding their structure and mechanism has been crucial to developing tools to control for, and occasionally even exploit, these particles. Unfortunately, their polydispersity and transient stability have prevented exploration of certain elementary properties, such as how they pack. Dye-stabilized colloidal aggregates exhibit enhanced homogeneity and stability when compared to conventional colloidal aggregates, enabling investigation of some of these properties. By small-angle X-ray scattering and multiangle light scattering, pair distance distribution functions suggest that the dye-stabilized colloids are filled, not hollow, spheres. Stability of the coformulated colloids enabled investigation of their preference for binding DNA, peptides, or folded proteins, and their ability to purify one from the other. The coformulated colloids showed little ability to bind DNA. Correspondingly, the colloids preferentially sequestered protein from even a 1600-fold excess of peptides that are themselves the result of a digest of the same protein. This may reflect the avidity advantage that a protein has in a surface-to-surface interaction with the colloids. For the first time, colloids could be shown to have preferences of up to 90-fold for particular proteins over others. Loaded onto the colloids, bound enzyme could be spun down, resuspended, and released back into buffer, regaining most of its activity. Implications of these observations for colloid mechanisms and utility will be considered.
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Affiliation(s)
- Da Duan
- Department of Pharmaceutical Chemistry & Quantitative Biology Institute, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94158-2550, United States
| | - Hayarpi Torosyan
- Department of Pharmaceutical Chemistry & Quantitative Biology Institute, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94158-2550, United States
| | - Daniel Elnatan
- Howard
Hughes Medical Institute and the Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158, United States
| | - Christopher K. McLaughlin
- Department
of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada M5S 3E5
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - Jennifer Logie
- Department
of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada M5S 3E5
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - Molly S. Shoichet
- Department
of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada M5S 3E5
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - David A. Agard
- Howard
Hughes Medical Institute and the Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158, United States
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry & Quantitative Biology Institute, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94158-2550, United States
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253
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Adhikary R, Zimmermann J, Romesberg FE. Transparent Window Vibrational Probes for the Characterization of Proteins With High Structural and Temporal Resolution. Chem Rev 2017; 117:1927-1969. [DOI: 10.1021/acs.chemrev.6b00625] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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254
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Cramer J, Schiebel J, Wulsdorf T, Grohe K, Najbauer EE, Ehrmann FR, Radeva N, Zitzer N, Linne U, Linser R, Heine A, Klebe G. A False-Positive Screening Hit in Fragment-Based Lead Discovery: Watch out for the Red Herring. Angew Chem Int Ed Engl 2017; 56:1908-1913. [PMID: 28097765 DOI: 10.1002/anie.201609824] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/24/2016] [Indexed: 01/08/2023]
Abstract
With the rising popularity of fragment-based approaches in drug development, more and more attention has to be devoted to the detection of false-positive screening results. In particular, the small size and low affinity of fragments drives screening techniques to their limit. The pursuit of a false-positive hit can cause significant loss of time and resources. Here, we present an instructive and intriguing investigation into the origin of misleading assay results for a fragment that emerged as the most potent binder for the aspartic protease endothiapepsin (EP) across multiple screening assays. This molecule shows its biological effect mainly after conversion into another entity through a reaction cascade that involves major rearrangements of its heterocyclic scaffold. The formed ligand binds EP through an induced-fit mechanism involving remarkable electrostatic interactions. Structural information in the initial screening proved to be crucial for the identification of this false-positive hit.
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Affiliation(s)
- Jonathan Cramer
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Johannes Schiebel
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Tobias Wulsdorf
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Kristof Grohe
- Abteilung für NMR-basierte Strukturbiologie, Max Planck Institut für Biophysikalische Chemie, Am Faßberg 11, 37077, Göttingen, Germany.,Fakultät für Chemie und Pharmazie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, Haus F, 81377, München, Germany
| | - Eszter Eva Najbauer
- Abteilung für NMR-basierte Strukturbiologie, Max Planck Institut für Biophysikalische Chemie, Am Faßberg 11, 37077, Göttingen, Germany
| | - Frederik R Ehrmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Nedyalka Radeva
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Nina Zitzer
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Uwe Linne
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043, Marburg, Germany
| | - Rasmus Linser
- Abteilung für NMR-basierte Strukturbiologie, Max Planck Institut für Biophysikalische Chemie, Am Faßberg 11, 37077, Göttingen, Germany.,Fakultät für Chemie und Pharmazie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, Haus F, 81377, München, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
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255
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Gilberg E, Stumpfe D, Bajorath J. Activity profiles of analog series containing pan assay interference compounds. RSC Adv 2017. [DOI: 10.1039/c7ra06736d] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Shown is the distribution of activity profiles (color-coded bars) of analog series containing PAINS substructures in a heatmap.
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Affiliation(s)
- Erik Gilberg
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
| | - Dagmar Stumpfe
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
| | - Jürgen Bajorath
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
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256
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257
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Mai S, Rao C, Chen M, Su J, Du J, Song Q. Merging gold catalysis, organocatalytic oxidation, and Lewis acid catalysis for chemodivergent synthesis of functionalized oxazoles from N-propargylamides. Chem Commun (Camb) 2017; 53:10366-10369. [DOI: 10.1039/c7cc05746f] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel catalytic systems consisting of cationic gold complexes, N-hydroxyphthalimide (NHPI), and transition-metal-based Lewis acids have been developed for the one-pot synthesis of functionalized oxazoles.
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Affiliation(s)
- Shaoyu Mai
- Institute of Next Generation Matter Transformation
- College of Chemical Engineering
- College of Material Sciences
- Huaqiao University
- Xiamen
| | - Changqing Rao
- Institute of Next Generation Matter Transformation
- College of Chemical Engineering
- College of Material Sciences
- Huaqiao University
- Xiamen
| | - Ming Chen
- CAS Key Laboratory of Microscale Magnetic Resonance
- Department of Modern Physics
- University of Science and Technology of China
- Hefei
- China
| | - Jihu Su
- CAS Key Laboratory of Microscale Magnetic Resonance
- Department of Modern Physics
- University of Science and Technology of China
- Hefei
- China
| | - Jiangfeng Du
- CAS Key Laboratory of Microscale Magnetic Resonance
- Department of Modern Physics
- University of Science and Technology of China
- Hefei
- China
| | - Qiuling Song
- Institute of Next Generation Matter Transformation
- College of Chemical Engineering
- College of Material Sciences
- Huaqiao University
- Xiamen
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258
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Dimova D, Gilberg E, Bajorath J. Identification and analysis of promiscuity cliffs formed by bioactive compounds and experimental implications. RSC Adv 2017. [DOI: 10.1039/c6ra27247a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
For three promiscuity cliffs (enclosed), cliff compounds, their promiscuity degrees (PDs), and color-coded substitution sites are shown. Comparison of these cliffs suggests the design of a new analog to further explore promiscuity.
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Affiliation(s)
- Dilyana Dimova
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
| | - Erik Gilberg
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
| | - Jürgen Bajorath
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
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259
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Shoombuatong W, Prathipati P, Owasirikul W, Worachartcheewan A, Simeon S, Anuwongcharoen N, Wikberg JES, Nantasenamat C. Towards the Revival of Interpretable QSAR Models. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2017. [DOI: 10.1007/978-3-319-56850-8_1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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260
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Wang Q, Liberti MV, Liu P, Deng X, Liu Y, Locasale JW, Lai L. Rational Design of Selective Allosteric Inhibitors of PHGDH and Serine Synthesis with Anti-tumor Activity. Cell Chem Biol 2016; 24:55-65. [PMID: 28042046 DOI: 10.1016/j.chembiol.2016.11.013] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 07/15/2016] [Accepted: 11/22/2016] [Indexed: 11/16/2022]
Abstract
Metabolic reprogramming in cancer cells facilitates growth and proliferation. Increased activity of the serine biosynthetic pathway through the enzyme phosphoglycerate dehydrogenase (PHGDH) contributes to tumorigenesis. With a small substrate and a weak binding cofactor, (NAD+), inhibitor development for PHGDH remains challenging. Instead of targeting the PHGDH active site, we computationally identified two potential allosteric sites and virtually screened compounds that can bind to these sites. With subsequent characterization, we successfully identified PHGDH non-NAD+-competing allosteric inhibitors that attenuate its enzyme activity, selectively inhibit de novo serine synthesis in cancer cells, and reduce tumor growth in vivo. Our study not only identifies novel allosteric inhibitors for PHGDH to probe its function and potential as a therapeutic target, but also provides a general strategy for the rational design of small-molecule modulators of metabolic enzyme function.
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Affiliation(s)
- Qian Wang
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Maria V Liberti
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Molecular Biology and Genetics, Graduate Field of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA
| | - Pei Liu
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaobing Deng
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Ying Liu
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Luhua Lai
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Center for Quantitative Biology, Peking University, Beijing 100871, China.
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261
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Tomek P, Palmer BD, Flanagan JU, Sun C, Raven EL, Ching LM. Discovery and evaluation of inhibitors to the immunosuppressive enzyme indoleamine 2,3-dioxygenase 1 (IDO1): Probing the active site-inhibitor interactions. Eur J Med Chem 2016; 126:983-996. [PMID: 28011425 DOI: 10.1016/j.ejmech.2016.12.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/30/2016] [Accepted: 12/12/2016] [Indexed: 01/21/2023]
Abstract
High expression of the immunosuppressive enzyme, indoleamine 2,3-dioxygenase 1 (IDO1) for a broad range of malignancies is associated with poor patient prognosis, and the enzyme is a validated target for cancer intervention. To identify novel IDO1 inhibitors suitable for drug development, 1597 compounds in the National Cancer Institute Diversity Set III library were tested for inhibitory activity against recombinant human IDO1. We retrieved 35 hits that inhibited IDO1 activity >50% at 20 μM. Five structural filters and the PubChem Bioassay database were used to guide the selection of five inhibitors with IC50 between 3 and 12 μM for subsequent experimental evaluation. A pyrimidinone scaffold emerged as being the most promising. It showed excellent cell penetration, negligible cytotoxicity and passed four out of the five structural filters applied. To evaluate the importance of Ser167 and Cys129 residues in the IDO1 active site for inhibitor binding, the entire NCI library was subsequently screened against alanine-replacement mutant enzymes of these two residues. The results established that Ser167 but not Cys129 is important for inhibitory activity of a broad range of IDO1 inhibitors. Structure-activity-relationship studies proposed substituents interacting with Ser167 on four investigated IDO1 inhibitors. Three of these four Ser167 interactions associated with an increased IDO1 inhibition and were correctly predicted by molecular docking supporting Ser167 as an important mediator of potency for IDO1 inhibitors.
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Affiliation(s)
- Petr Tomek
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, University of Auckland, New Zealand, Private Bag 92019, Victoria Street West, Auckland, New Zealand
| | - Brian D Palmer
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, University of Auckland, New Zealand, Private Bag 92019, Victoria Street West, Auckland, New Zealand
| | - Jack U Flanagan
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, University of Auckland, New Zealand, Private Bag 92019, Victoria Street West, Auckland, New Zealand
| | - Chuanwen Sun
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, University of Auckland, New Zealand, Private Bag 92019, Victoria Street West, Auckland, New Zealand
| | - Emma L Raven
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Lai-Ming Ching
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, University of Auckland, New Zealand, Private Bag 92019, Victoria Street West, Auckland, New Zealand.
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262
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Role of caffeine as an inhibitor in aggregation of hydrophobic molecules: A molecular dynamics simulation study. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.10.086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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263
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Han Y, Lyman KA, Clutter M, Schiltz GE, Ismail QA, Cheng X, Luan CH, Chetkovich DM. Method for Identifying Small Molecule Inhibitors of the Protein-protein Interaction Between HCN1 and TRIP8b. J Vis Exp 2016. [PMID: 27911380 DOI: 10.3791/54540] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are expressed ubiquitously throughout the brain, where they function to regulate the excitability of neurons. The subcellular distribution of these channels in pyramidal neurons of hippocampal area CA1 is regulated by tetratricopeptide repeat-containing Rab8b interacting protein (TRIP8b), an auxiliary subunit. Genetic knockout of HCN pore forming subunits or TRIP8b, both lead to an increase in antidepressant-like behavior, suggesting that limiting the function of HCN channels may be useful as a treatment for Major Depressive Disorder (MDD). Despite significant therapeutic interest, HCN channels are also expressed in the heart, where they regulate rhythmicity. To circumvent off-target issues associated with blocking cardiac HCN channels, our lab has recently proposed targeting the protein-protein interaction between HCN and TRIP8b in order to specifically disrupt HCN channel function in the brain. TRIP8b binds to HCN pore forming subunits at two distinct interaction sites, although here the focus is on the interaction between the tetratricopeptide repeat (TPR) domains of TRIP8b and the C terminal tail of HCN1. In this protocol, an expanded description of a method for purifying TRIP8b and executing a high throughput screen to identify small molecule inhibitors of the interaction between HCN and TRIP8b, is described. The method for high throughput screening utilizes a Fluorescence Polarization (FP) -based assay to monitor the binding of a large TRIP8b fragment to a fluorophore-tagged eleven amino acid peptide corresponding to the HCN1 C terminal tail. This method allows 'hit' compounds to be identified based on the change in the polarization of emitted light. Validation assays are then performed to ensure that 'hit' compounds are not artifactual.
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Affiliation(s)
- Ye Han
- Davee Department of Neurology and Clinical Neurosciences, Feinberg School of Medicine, Northwestern University;
| | - Kyle A Lyman
- Davee Department of Neurology and Clinical Neurosciences, Feinberg School of Medicine, Northwestern University
| | - Matt Clutter
- Center for Molecular Innovation and Drug Discovery, Northwestern University
| | - Gary E Schiltz
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University
| | - Quratul-Ain Ismail
- Davee Department of Neurology and Clinical Neurosciences, Feinberg School of Medicine, Northwestern University
| | - Xiangying Cheng
- Davee Department of Neurology and Clinical Neurosciences, Feinberg School of Medicine, Northwestern University
| | - Chi-Hao Luan
- High Throughput Analysis Laboratory, Department of Molecular Biosciences, Northwestern University
| | - Dane M Chetkovich
- Davee Department of Neurology and Clinical Neurosciences, Feinberg School of Medicine, Northwestern University; Department of Physiology, Feinberg School of Medicine, Northwestern University
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264
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Gilberg E, Jasial S, Stumpfe D, Dimova D, Bajorath J. Highly Promiscuous Small Molecules from Biological Screening Assays Include Many Pan-Assay Interference Compounds but Also Candidates for Polypharmacology. J Med Chem 2016; 59:10285-10290. [PMID: 27809519 DOI: 10.1021/acs.jmedchem.6b01314] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In PubChem screening assays, 466 highly promiscuous compounds were identified that were examined for known pan-assay interference compounds (PAINS) and aggregators using publicly available filters. These filters detected 210 PAINS and 67 aggregators. Compounds passing the filters included additional PAINS that were not detected, mostly due to tautomerism, and a variety of other potentially reactive compounds currently not encoded as PAINS. For a subset of compounds passing the filters, there was no evidence of potential artifacts. These compounds are considered candidates for further exploring multitarget activities and the molecular basis of polypharmacology.
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Affiliation(s)
- Erik Gilberg
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität , Dahlmannstrasse 2, D-53113 Bonn, Germany
| | - Swarit Jasial
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität , Dahlmannstrasse 2, D-53113 Bonn, Germany
| | - Dagmar Stumpfe
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität , Dahlmannstrasse 2, D-53113 Bonn, Germany
| | - Dilyana Dimova
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität , Dahlmannstrasse 2, D-53113 Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität , Dahlmannstrasse 2, D-53113 Bonn, Germany
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265
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Integrated Computational Approach for Virtual Hit Identification against Ebola Viral Proteins VP35 and VP40. Int J Mol Sci 2016; 17:ijms17111748. [PMID: 27792169 PMCID: PMC5133775 DOI: 10.3390/ijms17111748] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/18/2016] [Accepted: 09/22/2016] [Indexed: 12/30/2022] Open
Abstract
The Ebola virus (EBOV) has been recognised for nearly 40 years, with the most recent EBOV outbreak being in West Africa, where it created a humanitarian crisis. Mortalities reported up to 30 March 2016 totalled 11,307. However, up until now, EBOV drugs have been far from achieving regulatory (FDA) approval. It is therefore essential to identify parent compounds that have the potential to be developed into effective drugs. Studies on Ebola viral proteins have shown that some can elicit an immunological response in mice, and these are now considered essential components of a vaccine designed to protect against Ebola haemorrhagic fever. The current study focuses on chemoinformatic approaches to identify virtual hits against Ebola viral proteins (VP35 and VP40), including protein binding site prediction, drug-likeness, pharmacokinetic and pharmacodynamic properties, metabolic site prediction, and molecular docking. Retrospective validation was performed using a database of non-active compounds, and early enrichment of EBOV actives at different false positive rates was calculated. Homology modelling and subsequent superimposition of binding site residues on other strains of EBOV were carried out to check residual conformations, and hence to confirm the efficacy of potential compounds. As a mechanism for artefactual inhibition of proteins through non-specific compounds, virtual hits were assessed for their aggregator potential compared with previously reported aggregators. These systematic studies have indicated that a few compounds may be effective inhibitors of EBOV replication and therefore might have the potential to be developed as anti-EBOV drugs after subsequent testing and validation in experiments in vivo.
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266
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Cottet K, Xu B, Coric P, Bouaziz S, Michel S, Vidal M, Lallemand MC, Broussy S. Guttiferone A Aggregates Modulate Silent Information Regulator 1 (SIRT1) Activity. J Med Chem 2016; 59:9560-9566. [DOI: 10.1021/acs.jmedchem.6b01182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kévin Cottet
- Laboratoire
Pharmacognosie, Chimie des Substances Naturelles, Electrochimie UMR
COMETE 8638 CNRS, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, 4 Avenue de l’Observatoire, Paris 75006 France
| | - Bin Xu
- Laboratoire
Hétérocycles et Peptides: Approche Ciblée, Cancer
et Angiogenèse UMR COMETE 8638 CNRS, Faculté de Pharmacie
de Paris, Université Paris Descartes, Sorbonne Paris Cité, 4 Avenue
de l’Observatoire, Paris 75006 France
| | - Pascale Coric
- Laboratoire
de Cristallographie et RMN Biologiques, UMR 8015 CNRS, Faculté
de Pharmacie de Paris, Université Paris Descartes, Sorbonne
Paris Cité, 4 Avenue de l’Observatoire, Paris 75006 France
| | - Serge Bouaziz
- Laboratoire
de Cristallographie et RMN Biologiques, UMR 8015 CNRS, Faculté
de Pharmacie de Paris, Université Paris Descartes, Sorbonne
Paris Cité, 4 Avenue de l’Observatoire, Paris 75006 France
| | - Sylvie Michel
- Laboratoire
Pharmacognosie, Chimie des Substances Naturelles, Electrochimie UMR
COMETE 8638 CNRS, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, 4 Avenue de l’Observatoire, Paris 75006 France
| | - Michel Vidal
- Laboratoire
Hétérocycles et Peptides: Approche Ciblée, Cancer
et Angiogenèse UMR COMETE 8638 CNRS, Faculté de Pharmacie
de Paris, Université Paris Descartes, Sorbonne Paris Cité, 4 Avenue
de l’Observatoire, Paris 75006 France
- UF
Pharmacocinétique et Pharmacochimie, Hôpital Cochin, AP-HP, 27 Rue du Faubourg Saint Jacques, Paris 75014, France
| | - Marie-Christine Lallemand
- Laboratoire
Pharmacognosie, Chimie des Substances Naturelles, Electrochimie UMR
COMETE 8638 CNRS, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, 4 Avenue de l’Observatoire, Paris 75006 France
| | - Sylvain Broussy
- Laboratoire
Hétérocycles et Peptides: Approche Ciblée, Cancer
et Angiogenèse UMR COMETE 8638 CNRS, Faculté de Pharmacie
de Paris, Université Paris Descartes, Sorbonne Paris Cité, 4 Avenue
de l’Observatoire, Paris 75006 France
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267
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Strelow JM. A Perspective on the Kinetics of Covalent and Irreversible Inhibition. SLAS DISCOVERY 2016; 22:3-20. [PMID: 27703080 DOI: 10.1177/1087057116671509] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The clinical and commercial success of covalent drugs has prompted a renewed and more deliberate pursuit of covalent and irreversible mechanisms within drug discovery. A covalent mechanism can produce potent inhibition in a biochemical, cellular, or in vivo setting. In many cases, teams choose to focus on the consequences of the covalent event, defined by an IC50 value. In a biochemical assay, the IC50 may simply reflect the target protein concentration in the assay. What has received less attention is the importance of the rate of covalent modification, defined by kinact/KI. The kinact/KI is a rate constant describing the efficiency of covalent bond formation resulting from the potency (KI) of the first reversible binding event and the maximum potential rate (kinact) of inactivation. In this perspective, it is proposed that the kinact/KI should be employed as a critical parameter to identify covalent inhibitors, interpret structure-activity relationships (SARs), translate activity from biochemical assays to the cell, and more accurately define selectivity. It is also proposed that a physiologically relevant kinact/KI and an (unbound) AUC generated from a pharmacokinetic profile reflecting direct exposure of the inhibitor to the target protein are two critical determinants of in vivo covalent occupancy. A simple equation is presented to define this relationship and improve the interpretation of covalent and irreversible kinetics.
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Affiliation(s)
- John M Strelow
- 1 Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
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268
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Docking optimization, variance and promiscuity for large-scale drug-like chemical space using high performance computing architectures. Drug Discov Today 2016; 21:1672-1680. [DOI: 10.1016/j.drudis.2016.06.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/12/2016] [Accepted: 06/21/2016] [Indexed: 12/27/2022]
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269
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Dawei Z, Hongqiu H, Mengmeng L, Zhixia M, Shunxing G. A Novel Assay for Screening Inhibitors Targeting HIV Integrase LEDGF/p75 Interaction Based on Ni(2+) Coated Magnetic Agarose Beads. Sci Rep 2016; 6:33477. [PMID: 27633629 PMCID: PMC5025856 DOI: 10.1038/srep33477] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 08/24/2016] [Indexed: 01/04/2023] Open
Abstract
HIV-1 integrase (IN) plays an essential role in viral replication and thus serves as an important target for chemotherapeutic intervention against HIV-1 infection. However, the current three clinical IN inhibitors, raltegravir, elvitegravir and dolutegravir share the same inhibitory mechanism, resulting in a common clinical resistance profile which have emerged in infected patients receiving treatment. Therefore, it is important to develop small molecule inhibitors that impair IN function with distinct mechanisms of action. In this work, a magnetic-beads based biochemical assay targeting the protein-protein interaction (PPI) between HIV IN and the cellular cofactor LEDGF/p75 was developed for identification of HIV-1 IN inhibitors. Furthermore, a library containing 1000 US. Food and Drug Administration (FDA)-approved drugs currently used for human medication was screened to identify inhibitors targeting the PPI. The assay was proved to be quite robust and with the novel assay we successfully identified dexlansoprazole (IC50 of 4.8 μM), a FDA-approved proton pump inhibitor, as a potential inhibitor for the PPI between IN and LEDGF/p75, which bound to the LEDGF/p75 partner with a kinetic dissociation (Kd) constant of 330 nM ± 2.6 nM.
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Affiliation(s)
- Zhang Dawei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, 100193, China.,Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - He Hongqiu
- Chongqing Center for Biomedicines and Medical Equipment, Chongqing Academy of Science and Technology, Chongqing, 401123, China
| | - Liu Mengmeng
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, 100193, China.,Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Meng Zhixia
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, 100193, China
| | - Guo Shunxing
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing, 100193, China
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270
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Sharma B, Paul S. Action of Caffeine as an Amyloid Inhibitor in the Aggregation of Aβ16–22 Peptides. J Phys Chem B 2016; 120:9019-33. [DOI: 10.1021/acs.jpcb.6b03892] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Bhanita Sharma
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, Assam, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, Assam, India
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271
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Winton VJ, Aldrich C, Kiessling LL. Carboxylate Surrogates Enhance the Antimycobacterial Activity of UDP-Galactopyranose Mutase Probes. ACS Infect Dis 2016; 2:538-43. [PMID: 27626294 DOI: 10.1021/acsinfecdis.6b00021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Uridine diphosphate galactopyranose mutase (UGM also known as Glf) is a biosynthetic enzyme required for construction of the galactan, an essential mycobacterial cell envelope polysaccharide. Our group previously identified two distinct classes of UGM inhibitors; each possesses a carboxylate moiety that is crucial for potency yet likely detrimental for cell permeability. To enhance the antimycobacterial potency, we sought to replace the carboxylate with a functional group mimic-an N-acylsulfonamide group. We therefore synthesized a series of N-acylsulfonamide analogs and tested their ability to inhibit UGM. For each inhibitor scaffold tested, the N-acylsulfonamide group functions as an effective carboxylate surrogate. Although the carboxylates and their surrogates show similar activity against UGM in a test tube, several N-acylsulfonamide derivatives more effectively block the growth of Mycobacterium smegmatis. These data suggest that the replacement of a carboxylate with an N-acylsulfonamide group could serve as a general strategy to augment antimycobacterial activity.
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Affiliation(s)
- Valerie J. Winton
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - Claudia Aldrich
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - Laura L. Kiessling
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
- Department
of Biochemistry, University of Wisconsin—Madison, 433 Babcock Drive, Madison, Wisconsin 53706-1544, United States
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272
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Lacroix C, Fish I, Torosyan H, Parathaman P, Irwin JJ, Shoichet BK, Angers S. Identification of Novel Smoothened Ligands Using Structure-Based Docking. PLoS One 2016; 11:e0160365. [PMID: 27490099 PMCID: PMC4973902 DOI: 10.1371/journal.pone.0160365] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 07/18/2016] [Indexed: 12/21/2022] Open
Abstract
The seven transmembrane protein Smoothened is required for Hedgehog signaling during embryonic development and adult tissue homeostasis. Inappropriate activation of the Hedgehog signalling pathway leads to cancers such as basal cell carcinoma and medulloblastoma, and Smoothened inhibitors are now available clinically to treat these diseases. However, resistance to these inhibitors rapidly develops thereby limiting their efficacy. The determination of Smoothened crystal structures enables structure-based discovery of new ligands with new chemotypes that will be critical to combat resistance. In this study, we docked 3.2 million available, lead-like molecules against Smoothened, looking for those with high physical complementarity to its structure; this represents the first such campaign against the class Frizzled G-protein coupled receptor family. Twenty-one high-ranking compounds were selected for experimental testing, and four, representing three different chemotypes, were identified to antagonize Smoothened with IC50 values better than 50 μM. A screen for analogs revealed another six molecules, with IC50 values in the low micromolar range. Importantly, one of the most active of the new antagonists continued to be efficacious at the D473H mutant of Smoothened, which confers clinical resistance to the antagonist vismodegib in cancer treatment.
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Affiliation(s)
- Celine Lacroix
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Inbar Fish
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat Aviv, Israel
| | - Hayarpi Torosyan
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Pranavan Parathaman
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - John J. Irwin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (BS); (SA)
| | - Stephane Angers
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (BS); (SA)
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273
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Abstract
After 20 years of sometimes quiet growth, fragment-based drug discovery (FBDD) has become mainstream. More than 30 drug candidates derived from fragments have entered the clinic, with two approved and several more in advanced trials. FBDD has been widely applied in both academia and industry, as evidenced by the large number of papers from universities, non-profit research institutions, biotechnology companies and pharmaceutical companies. Moreover, FBDD draws on a diverse range of disciplines, from biochemistry and biophysics to computational and medicinal chemistry. As the promise of FBDD strategies becomes increasingly realized, now is an opportune time to draw lessons and point the way to the future. This Review briefly discusses how to design fragment libraries, how to select screening techniques and how to make the most of information gleaned from them. It also shows how concepts from FBDD have permeated and enhanced drug discovery efforts.
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274
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Xanthopoulos D, Kritsi E, Supuran CT, Papadopoulos MG, Leonis G, Zoumpoulakis P. Discovery of HIV Type 1 Aspartic Protease Hit Compounds through Combined Computational Approaches. ChemMedChem 2016; 11:1646-52. [PMID: 27411556 DOI: 10.1002/cmdc.201600220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/07/2016] [Indexed: 12/28/2022]
Abstract
A combination of computational techniques and inhibition assay experiments was employed to identify hit compounds from commercial libraries with enhanced inhibitory potency against HIV type 1 aspartic protease (HIV PR). Extensive virtual screening with the aid of reliable pharmacophore models yielded five candidate protease inhibitors. Subsequent molecular dynamics and molecular mechanics Poisson-Boltzmann surface area free-energy calculations for the five ligand-HIV PR complexes suggested a high stability of the systems through hydrogen-bond interactions between the ligands and the protease's flaps (Ile50/50'), as well as interactions with residues of the active site (Asp25/25'/29/29'/30/30'). Binding-energy calculations for the three most promising compounds yielded values between -5 and -10 kcal mol(-1) and suggested that van der Waals interactions contribute most favorably to the total energy. The predicted binding-energy values were verified by in vitro inhibition assays, which showed promising results in the high nanomolar range. These results provide structural considerations that may guide further hit-to-lead optimization toward improved anti-HIV drugs.
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Affiliation(s)
- Dimitrios Xanthopoulos
- National Hellenic Research Foundation (NHRF), Institute of Biology, Medicinal Chemistry and Biotechnology (IBMCB), Vassileos-Constantinou-Ave. 48, 11635, Athens, Greece
| | - Eftichia Kritsi
- National Hellenic Research Foundation (NHRF), Institute of Biology, Medicinal Chemistry and Biotechnology (IBMCB), Vassileos-Constantinou-Ave. 48, 11635, Athens, Greece.,School of Chemical Engineering, National Technical University of Athens (NTUA), Organic Synthesis Laboratory, Iroon-Polytechneiou-Str. 9, 15773, Athens, Greece
| | - Claudiu T Supuran
- Neurofarba Dept., Sezione di Scienze farmaceutiche e nutraceutiche, e Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze, Rm. 188, Via UgoSchiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Manthos G Papadopoulos
- National Hellenic Research Foundation (NHRF), Institute of Biology, Medicinal Chemistry and Biotechnology (IBMCB), Vassileos-Constantinou-Ave. 48, 11635, Athens, Greece
| | - Georgios Leonis
- National Hellenic Research Foundation (NHRF), Institute of Biology, Medicinal Chemistry and Biotechnology (IBMCB), Vassileos-Constantinou-Ave. 48, 11635, Athens, Greece.
| | - Panagiotis Zoumpoulakis
- National Hellenic Research Foundation (NHRF), Institute of Biology, Medicinal Chemistry and Biotechnology (IBMCB), Vassileos-Constantinou-Ave. 48, 11635, Athens, Greece.
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275
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Discovery of a novel covalent non-β-lactam inhibitor of the metallo-β-lactamase NDM-1. Bioorg Med Chem 2016; 24:2947-2953. [DOI: 10.1016/j.bmc.2016.04.064] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 04/28/2016] [Accepted: 04/30/2016] [Indexed: 02/05/2023]
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276
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Interpreting the behavior of concentration–response curves of hyaluronidase inhibitors under DMSO-perturbed assay conditions. Bioorg Med Chem Lett 2016; 26:3153-3157. [DOI: 10.1016/j.bmcl.2016.04.082] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 04/26/2016] [Accepted: 04/28/2016] [Indexed: 11/22/2022]
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277
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Nikiforov VN, Vinogradov SE, Ivanov AV, Efremova EV, Kalnina LB, Bychenko AB, Tentsov YY, Manykin AA. Application of Laser Correlation Spectroscopy for Measuring Virus Size. Bull Exp Biol Med 2016; 161:88-91. [PMID: 27270934 DOI: 10.1007/s10517-016-3352-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Indexed: 11/28/2022]
Abstract
Dynamic light scattering method or laser correlation spectroscopy was applied to evaluation of the size of viruses. We measured correlation functions of the light scattered by human immunodeficiency viruses (HIV) and hepatitis A viruses (HAV) and found that size of HIV-1 (subtype A and B) and HAV virions were 104 nm and 28 nm, respectively. Comparison of these findings with electron microscopy data for fixed samples of the same viruses showed good agreement of the results.
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Affiliation(s)
- V N Nikiforov
- Physical Faculty, M. V. Lomonosov Moscow State University, Moscow, Russia.
| | - S E Vinogradov
- N. N. Blokhin Russian Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia
| | - A V Ivanov
- N. N. Blokhin Russian Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia
| | - E V Efremova
- D. I. Ivanovsky Institute of Virology, N. F. Gamaleya Federal Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - L B Kalnina
- D. I. Ivanovsky Institute of Virology, N. F. Gamaleya Federal Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - A B Bychenko
- M. P. Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Yu Yu Tentsov
- D. I. Ivanovsky Institute of Virology, N. F. Gamaleya Federal Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - A A Manykin
- D. I. Ivanovsky Institute of Virology, N. F. Gamaleya Federal Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
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278
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Hu Y, Bajorath J. Analyzing compound activity records and promiscuity degrees in light of publication statistics. F1000Res 2016; 5. [PMID: 27347396 PMCID: PMC4916991 DOI: 10.12688/f1000research.8792.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/05/2016] [Indexed: 11/25/2022] Open
Abstract
For the generation of contemporary databases of bioactive compounds, activity information is usually extracted from the scientific literature. However, when activity data are analyzed, source publications are typically no longer taken into consideration. Therefore, compound activity data selected from ChEMBL were traced back to thousands of original publications, activity records including compound, assay, and target information were systematically generated, and their distributions across the literature were determined. In addition, publications were categorized on the basis of activity records. Furthermore, compound promiscuity, defined as the ability of small molecules to specifically interact with multiple target proteins, was analyzed in light of publication statistics, thus adding another layer of information to promiscuity assessment. It was shown that the degree of compound promiscuity was not influenced by increasing numbers of source publications. Rather, most non-promiscuous as well as promiscuous compounds, regardless of their degree of promiscuity, originated from single publications, which emerged as a characteristic feature of the medicinal chemistry literature.
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Affiliation(s)
- Ye Hu
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, D-53113, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, D-53113, Germany
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279
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Valiente-Gabioud AA, Miotto MC, Chesta ME, Lombardo V, Binolfi A, Fernández CO. Phthalocyanines as Molecular Scaffolds to Block Disease-Associated Protein Aggregation. Acc Chem Res 2016; 49:801-8. [PMID: 27136297 DOI: 10.1021/acs.accounts.5b00507] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The aggregation of proteins into toxic conformations plays a critical role in the development of different neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), and Creutzfled-Jakob's disease (CJD). These disorders share a common pathological mechanism that involves the formation of aggregated protein species including toxic oligomers and amyloid fibrils. The aggregation of alpha-synuclein (αS) in PD and the amyloid beta peptide (Aβ) and tau protein in AD results in neuronal death and disease onset. In the case of CJD, the misfolding of the physiological prion protein (PrP) induces a chain reaction that results in accumulation of particles that elicit brain damage. Currently, there is no preventive therapy for these diseases and the available therapeutic approaches are based on the treatment of the symptoms rather than the underlying causes of the disease. Accordingly, the aggregation pathway of these proteins represents a useful target for therapeutic intervention. Therefore, understanding the mechanism of amyloid formation and its inhibition is of high clinical importance. The design of small molecules that efficiently inhibit the aggregation process and/or neutralize its associated toxicity constitutes a promising tool for the development of therapeutic strategies against these disorders. In this accounts, we discuss current knowledge on the anti-amyloid activity of phthalocyanines and their potential use as drug candidates in neurodegeneration. These tetrapyrrolic compounds modulate the amyloid assembly of αS, tau, Aβ, and the PrP in vitro, and protect cells from the toxic effects of amyloid aggregates. In addition, in scrapie-infected mice, these compounds showed important prophylactic antiscrapie properties. The structural basis for the inhibitory effect of phthalocyanines on amyloid filament assembly relies on specific π-π interactions between the aromatic ring system of these molecules and aromatic residues in the amyloidogenic proteins. Analysis of the structure-activity relationship in phthalocyanines revealed that their anti-amyloid activity is highly dependent on the type of metal ion coordinated to the tetrapyrrolic system but is not sensitive to the number of peripheral charged substituents. The tendency of phthalocyanines to oligomerize (self-association) via aromatic-aromatic stacking interactions correlates precisely with their binding capabilities to target proteins and, more importantly, determines their efficiency as anti-amyloid agents. The ability to block different types of disease-associated protein aggregation raises the possibility that these cyclic tetrapyrrole compounds have a common mechanism of action to impair the formation of a variety of pathological aggregates. Because the structural and molecular basis for the anti-amyloid effects of these molecules is starting to emerge, combined efforts from the fields of structural, cellular, and animal biology will result critical for the rational design and discovery of new drugs for the treatment of amyloid related neurological disorders.
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Affiliation(s)
- Ariel A. Valiente-Gabioud
- Max Planck Laboratory for Structural Biology,
Chemistry and Molecular
Biophysics of Rosario (MPLbioR, UNR-MPIbpC) and ‡Instituto de Investigaciones para
el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario, Ocampo y Esmeralda, S2002LRK Rosario, Argentina
| | - Marco C. Miotto
- Max Planck Laboratory for Structural Biology,
Chemistry and Molecular
Biophysics of Rosario (MPLbioR, UNR-MPIbpC) and ‡Instituto de Investigaciones para
el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario, Ocampo y Esmeralda, S2002LRK Rosario, Argentina
| | - María E. Chesta
- Max Planck Laboratory for Structural Biology,
Chemistry and Molecular
Biophysics of Rosario (MPLbioR, UNR-MPIbpC) and ‡Instituto de Investigaciones para
el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario, Ocampo y Esmeralda, S2002LRK Rosario, Argentina
| | - Verónica Lombardo
- Max Planck Laboratory for Structural Biology,
Chemistry and Molecular
Biophysics of Rosario (MPLbioR, UNR-MPIbpC) and ‡Instituto de Investigaciones para
el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario, Ocampo y Esmeralda, S2002LRK Rosario, Argentina
| | - Andres Binolfi
- Max Planck Laboratory for Structural Biology,
Chemistry and Molecular
Biophysics of Rosario (MPLbioR, UNR-MPIbpC) and ‡Instituto de Investigaciones para
el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario, Ocampo y Esmeralda, S2002LRK Rosario, Argentina
| | - Claudio O. Fernández
- Max Planck Laboratory for Structural Biology,
Chemistry and Molecular
Biophysics of Rosario (MPLbioR, UNR-MPIbpC) and ‡Instituto de Investigaciones para
el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario, Ocampo y Esmeralda, S2002LRK Rosario, Argentina
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280
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Malik EM, Müller CE. Anthraquinones As Pharmacological Tools and Drugs. Med Res Rev 2016; 36:705-48. [PMID: 27111664 DOI: 10.1002/med.21391] [Citation(s) in RCA: 247] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/09/2016] [Accepted: 02/27/2016] [Indexed: 12/11/2022]
Abstract
Anthraquinones (9,10-dioxoanthracenes) constitute an important class of natural and synthetic compounds with a wide range of applications. Besides their utilization as colorants, anthraquinone derivatives have been used since centuries for medical applications, for example, as laxatives and antimicrobial and antiinflammatory agents. Current therapeutic indications include constipation, arthritis, multiple sclerosis, and cancer. Moreover, biologically active anthraquinones derived from Reactive Blue 2 have been utilized as valuable tool compounds for biochemical and pharmacological studies. They may serve as lead structures for the development of future drugs. However, the presence of the quinone moiety in the structure of anthraquinones raises safety concerns, and anthraquinone laxatives have therefore been under critical reassessment. This review article provides an overview of the chemistry, biology, and toxicology of anthraquinones focusing on their application as drugs.
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Affiliation(s)
- Enas M Malik
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, Pharmaceutical Sciences Bonn (PSB), University of Bonn, An der Immenburg 4, D-53121, Bonn, Germany
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, Pharmaceutical Sciences Bonn (PSB), University of Bonn, An der Immenburg 4, D-53121, Bonn, Germany
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281
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McLaughlin CK, Duan D, Ganesh AN, Torosyan H, Shoichet BK, Shoichet MS. Stable Colloidal Drug Aggregates Catch and Release Active Enzymes. ACS Chem Biol 2016; 11:992-1000. [PMID: 26741163 DOI: 10.1021/acschembio.5b00806] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Small molecule aggregates are considered nuisance compounds in drug discovery, but their unusual properties as colloids could be exploited to form stable vehicles to preserve protein activity. We investigated the coaggregation of seven molecules chosen because they had been previously intensely studied as colloidal aggregators, coformulating them with bis-azo dyes. The coformulation reduced colloid sizes to <100 nm and improved uniformity of the particle size distribution. The new colloid formulations are more stable than previous aggregator particles. Specifically, coaggregation of Congo Red with sorafenib, tetraiodophenolphthalein (TIPT), or vemurafenib produced particles that are stable in solutions of high ionic strength and high protein concentrations. Like traditional, single compound colloidal aggregates, the stabilized colloids adsorbed and inhibited enzymes like β-lactamase, malate dehydrogenase, and trypsin. Unlike traditional aggregates, the coformulated colloid-protein particles could be centrifuged and resuspended multiple times, and from resuspended particles, active trypsin could be released up to 72 h after adsorption. Unexpectedly, the stable colloidal formulations can sequester, stabilize, and isolate enzymes by spin-down, resuspension, and release.
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Affiliation(s)
- Christopher K. McLaughlin
- Department
of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada M5S 3E5
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - Da Duan
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94158-2550, United States
| | - Ahil N. Ganesh
- Department
of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada M5S 3E5
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - Hayarpi Torosyan
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94158-2550, United States
| | - Brian K. Shoichet
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94158-2550, United States
| | - Molly S. Shoichet
- Department
of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada M5S 3E5
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
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282
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Abstract
It is now plausible to dock libraries of 10 million molecules against targets over several days or weeks. When the molecules screened are commercially available, they may be rapidly tested to find new leads. Although docking retains important liabilities (it cannot calculate affinities accurately nor even reliably rank order high-scoring molecules), it can often can distinguish likely from unlikely ligands, often with hit rates above 10%. Here we summarize the improvements in libraries, target quality, and methods that have supported these advances, and the open access resources that make docking accessible. Recent docking screens for new ligands are sketched, as are the binding, crystallographic, and in vivo assays that support them. Like any technique, controls are crucial, and key experimental ones are reviewed. With such controls, docking campaigns can find ligands with new chemotypes, often revealing the new biology that may be docking's greatest impact over the next few years.
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Affiliation(s)
- John J Irwin
- Department of Pharmaceutical Chemistry and QB3 Institute, University of California-San Francisco , San Francisco, California 94158, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry and QB3 Institute, University of California-San Francisco , San Francisco, California 94158, United States
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283
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Farrell MS, McCorvy JD, Huang XP, Urban DJ, White KL, Giguere PM, Doak AK, Bernstein AI, Stout KA, Park SM, Rodriguiz RM, Gray BW, Hyatt WS, Norwood AP, Webster KA, Gannon BM, Miller GW, Porter JH, Shoichet BK, Fantegrossi WE, Wetsel WC, Roth BL. In Vitro and In Vivo Characterization of the Alkaloid Nuciferine. PLoS One 2016; 11:e0150602. [PMID: 26963248 PMCID: PMC4786259 DOI: 10.1371/journal.pone.0150602] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 02/17/2016] [Indexed: 01/05/2023] Open
Abstract
Rationale The sacred lotus (Nelumbo nucifera) contains many phytochemicals and has a history of human use. To determine which compounds may be responsible for reported psychotropic effects, we used in silico predictions of the identified phytochemicals. Nuciferine, an alkaloid component of Nelumbo nucifera and Nymphaea caerulea, had a predicted molecular profile similar to antipsychotic compounds. Our study characterizes nuciferine using in vitro and in vivo pharmacological assays. Methods Nuciferine was first characterized in silico using the similarity ensemble approach, and was followed by further characterization and validation using the Psychoactive Drug Screening Program of the National Institute of Mental Health. Nuciferine was then tested in vivo in the head-twitch response, pre-pulse inhibition, hyperlocomotor activity, and drug discrimination paradigms. Results Nuciferine shares a receptor profile similar to aripiprazole-like antipsychotic drugs. Nuciferine was an antagonist at 5-HT2A, 5-HT2C, and 5-HT2B, an inverse agonist at 5-HT7, a partial agonist at D2, D5 and 5-HT6, an agonist at 5-HT1A and D4 receptors, and inhibited the dopamine transporter. In rodent models relevant to antipsychotic drug action, nuciferine blocked head-twitch responses and discriminative stimulus effects of a 5-HT2A agonist, substituted for clozapine discriminative stimulus, enhanced amphetamine induced locomotor activity, inhibited phencyclidine (PCP)-induced locomotor activity, and rescued PCP-induced disruption of prepulse inhibition without induction of catalepsy. Conclusions The molecular profile of nuciferine was similar but not identical to that shared with several approved antipsychotic drugs suggesting that nuciferine has atypical antipsychotic-like actions.
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Affiliation(s)
- Martilias S. Farrell
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- * E-mail:
| | - John D. McCorvy
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Daniel J. Urban
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Kate L. White
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Patrick M. Giguere
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Allison K. Doak
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Alison I. Bernstein
- Department of Environmental Health, Rollins School of Public Health and Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, United States of America
| | - Kristen A. Stout
- Department of Environmental Health, Rollins School of Public Health and Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, United States of America
| | - Su Mi Park
- Departments of Psychiatry and Behavioral Sciences, Cell Biology, and Neurobiology, Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Ramona M. Rodriguiz
- Departments of Psychiatry and Behavioral Sciences, Cell Biology, and Neurobiology, Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Bradley W. Gray
- Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - William S. Hyatt
- Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Andrew P. Norwood
- Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Kevin A. Webster
- Department of Psychology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Brenda M. Gannon
- Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Gary W. Miller
- Department of Environmental Health, Rollins School of Public Health and Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, United States of America
| | - Joseph H. Porter
- Department of Psychology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - William E. Fantegrossi
- Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - William C. Wetsel
- Departments of Psychiatry and Behavioral Sciences, Cell Biology, and Neurobiology, Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Bryan L. Roth
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- Program in Neuroscience, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- Carolina Institute for Developmental Disabilities, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- Division of Chemical Biology and Medicinal Chemistry, School of Pharmacy, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
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284
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Prade E, Barucker C, Sarkar R, Althoff-Ospelt G, Lopez del Amo JM, Hossain S, Zhong Y, Multhaup G, Reif B. Sulindac Sulfide Induces the Formation of Large Oligomeric Aggregates of the Alzheimer's Disease Amyloid-β Peptide Which Exhibit Reduced Neurotoxicity. Biochemistry 2016; 55:1839-49. [PMID: 26900939 DOI: 10.1021/acs.biochem.5b01272] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alzheimer's disease is characterized by deposition of the amyloid β-peptide (Aβ) in brain tissue of affected individuals. In recent years, many potential lead structures have been suggested that can potentially be used for diagnosis and therapy. However, the mode of action of these compounds is so far not understood. Among these small molecules, the nonsteroidal anti-inflammatory drug (NSAID) sulindac sulfide received a lot of attention. In this manuscript, we characterize the interaction between the monomeric Aβ peptide and the NSAID sulindac sulfide. We find that sulindac sulfide efficiently depletes the pool of toxic oligomers by enhancing the rate of fibril formation. In vitro, sulindac sulfide forms colloidal particles which catalyze the formation of fibrils. Aggregation is immediate, presumably by perturbing the supersaturated Aβ solution. We find that sulindac sulfide induced Aβ aggregates are structurally homogeneous. The C-terminal part of the peptide adopts a β-sheet structure, whereas the N-terminus is disordered. The salt bridge between D23 and K28 is present, similar as in wild type fibril structures. (13)C-(19)F transferred echo double resonance experiments suggest that sulindac sulfide colocalizes with the Aβ peptide in the aggregate.
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Affiliation(s)
- Elke Prade
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM) , Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Christian Barucker
- Department of Pharmacology & Therapeutics, McGill University , 3655 Promenade Sir-William-Osler, Montreal, Quebec H3G 1Y6, Canada
| | - Riddhiman Sarkar
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM) , Lichtenbergstrasse 4, 85747 Garching, Germany
| | | | - Juan Miguel Lopez del Amo
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Shireen Hossain
- Department of Pharmacology & Therapeutics, McGill University , 3655 Promenade Sir-William-Osler, Montreal, Quebec H3G 1Y6, Canada
| | - Yifei Zhong
- Department of Pharmacology & Therapeutics, McGill University , 3655 Promenade Sir-William-Osler, Montreal, Quebec H3G 1Y6, Canada
| | - Gerd Multhaup
- Department of Pharmacology & Therapeutics, McGill University , 3655 Promenade Sir-William-Osler, Montreal, Quebec H3G 1Y6, Canada
| | - Bernd Reif
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM) , Lichtenbergstrasse 4, 85747 Garching, Germany.,Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
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285
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Long L, Li W, Chen W, Li FF, Li H, Wang LL. Dynamic cytotoxic profiles of sulfur mustard in human dermal cells determined by multiparametric high-content analysis. Toxicol Res (Camb) 2016; 5:583-593. [PMID: 30090372 PMCID: PMC6062398 DOI: 10.1039/c5tx00305a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 01/10/2016] [Indexed: 01/01/2023] Open
Abstract
Sulfur mustard (SM) is a well known chemical warfare agent that poses a major threat to military personnel and also populace. It targets multiple macromolecules, and its toxic effects are mediated by complex mechanisms. However, the sequence and manner of SM-induced cellular and molecular events underpinning the pathological processes are not fully elucidated. Effective therapeutic agents against SM poisoning are also lacking. The present study aimed to determine the dynamic cytotoxic profiles of SM in primary cultured human epidermal keratinocytes-fetal (HEK-f) and human dermal fibroblasts-adult (HDF-a) by establishing a high content analysis (HCA)-based multiparametric toxicity assay panel. SM was found to produce multiple, concentration-dependent cellular responses, including abnormal cellular morphology, cycle arrest, apoptosis, necrosis, mitochondrial membrane potential imbalance, increased membrane permeability, oxidative stress, DNA damage, and lysosome impairment. Time-course analysis indicated that the cellular and molecular responses related to the highly reactive targets of SM, such as glutathione depletion, reactive oxygen species release, DNA and lysosomal damage, and actin microfilament architecture modification, were congenerous initial events for SM injury. Moreover, this study demonstrated a novel finding that SM induced autophagy, and it was closely related to lysosome alterations in both cell types. Higher susceptibility of HEK-f cells to SM was associated with early lysosomal damage and decreased autophagy activity. Multiparametric HCA also revealed the concentration-dependent cytoprotective effect of hydroxychloroquine in HDF-a cells. The above results provided overall and objective evidence for elucidating the cytotoxic mechanism of SM, and also a good scientific base for further research on countermeasures against SM injury.
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Affiliation(s)
- Long Long
- State Key Laboratory of Toxicology and Medical Countermeasures , Beijing , 100850 , China
- Beijing Institute of Pharmacology and Toxicology , Beijing , 100850 , China . ; ; ; Tel: +81-10-6821-0866
| | - Wei Li
- State Key Laboratory of Toxicology and Medical Countermeasures , Beijing , 100850 , China
- Beijing Institute of Pharmacology and Toxicology , Beijing , 100850 , China . ; ; ; Tel: +81-10-6821-0866
| | - Wei Chen
- State Key Laboratory of Toxicology and Medical Countermeasures , Beijing , 100850 , China
- Beijing Institute of Pharmacology and Toxicology , Beijing , 100850 , China . ; ; ; Tel: +81-10-6821-0866
| | - Fei-Fei Li
- State Key Laboratory of Toxicology and Medical Countermeasures , Beijing , 100850 , China
- Beijing Institute of Pharmacology and Toxicology , Beijing , 100850 , China . ; ; ; Tel: +81-10-6821-0866
| | - Hua Li
- State Key Laboratory of Toxicology and Medical Countermeasures , Beijing , 100850 , China
- Beijing Institute of Pharmacology and Toxicology , Beijing , 100850 , China . ; ; ; Tel: +81-10-6821-0866
| | - Li-Li Wang
- State Key Laboratory of Toxicology and Medical Countermeasures , Beijing , 100850 , China
- Beijing Institute of Pharmacology and Toxicology , Beijing , 100850 , China . ; ; ; Tel: +81-10-6821-0866
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286
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Jackson MJ, Kestur US, Hussain MA, Taylor LS. Characterization of Supersaturated Danazol Solutions – Impact of Polymers on Solution Properties and Phase Transitions. Pharm Res 2016; 33:1276-88. [DOI: 10.1007/s11095-016-1871-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 02/02/2016] [Indexed: 11/24/2022]
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287
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Hu H, Qian K, Ho MC, Zheng YG. Small Molecule Inhibitors of Protein Arginine Methyltransferases. Expert Opin Investig Drugs 2016; 25:335-58. [PMID: 26789238 DOI: 10.1517/13543784.2016.1144747] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
INTRODUCTION Arginine methylation is an abundant posttranslational modification occurring in mammalian cells and catalyzed by protein arginine methyltransferases (PRMTs). Misregulation and aberrant expression of PRMTs are associated with various disease states, notably cancer. PRMTs are prominent therapeutic targets in drug discovery. AREAS COVERED The authors provide an updated review of the research on the development of chemical modulators for PRMTs. Great efforts are seen in screening and designing potent and selective PRMT inhibitors, and a number of micromolar and submicromolar inhibitors have been obtained for key PRMT enzymes such as PRMT1, CARM1, and PRMT5. The authors provide a focus on their chemical structures, mechanism of action, and pharmacological activities. Pros and cons of each type of inhibitors are also discussed. EXPERT OPINION Several key challenging issues exist in PRMT inhibitor discovery. Structural mechanisms of many PRMT inhibitors remain unclear. There lacks consistency in potency data due to divergence of assay methods and conditions. Physiologically relevant cellular assays are warranted. Substantial engagements are needed to investigate pharmacodynamics and pharmacokinetics of the new PRMT inhibitors in pertinent disease models. Discovery and evaluation of potent, isoform-selective, cell-permeable and in vivo-active PRMT modulators will continue to be an active arena of research in years ahead.
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Affiliation(s)
- Hao Hu
- a Department of Pharmaceutical and Biomedical Sciences , The University of Georgia , Athens , GA , USA
| | - Kun Qian
- a Department of Pharmaceutical and Biomedical Sciences , The University of Georgia , Athens , GA , USA
| | - Meng-Chiao Ho
- b Institute of Biological Chemistry , Academia Sinica , Nankang , Taipei , Taiwan
| | - Y George Zheng
- a Department of Pharmaceutical and Biomedical Sciences , The University of Georgia , Athens , GA , USA
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288
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Zhou J, Du X, Xu B. Prion-like nanofibrils of small molecules (PriSM): A new frontier at the intersection of supramolecular chemistry and cell biology. Prion 2016; 9:110-8. [PMID: 25738892 DOI: 10.1080/19336896.2015.1022021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Formed by non-covalent interactions and not defined at genetic level, the assemblies of small molecules in biology are complicated and less explored. A common morphology of the supramolecular assemblies of small molecules is nanofibrils, which coincidentally resembles the nanofibrils formed by proteins such as prions. So these supramolecular assemblies are termed as prion-like nanofibrils of small molecules (PriSM). Emerging evidence from several unrelated fields over the past decade implies the significance of PriSM in biology and medicine. This perspective aims to highlight some recent advances of the research on PriSM. This paper starts with description of the intriguing similarities between PriSM and prions, discusses the paradoxical features of PriSM, introduces the methods for elucidating the biological functions of PriSM, illustrates several examples of beneficial aspects of PriSM, and finishes with the promises and current challenges in the research of PriSM. We anticipate that the research of PriSM will contribute to the fundamental understanding at the intersection of supramolecular chemistry and cell biology and ultimately lead to a new paradigm of molecular (or supramolecular) therapeutics for biomedicine.
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Affiliation(s)
- Jie Zhou
- a Department of Chemistry ; Brandeis University ; Waltham , MA USA
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289
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Abstract
Cisplatin and other platinum compounds have had a huge impact in the treatment of cancers and are applied in the majority of anticancer chemotherapeutic regimens. The success of these compounds has biased the approaches used to discover new metal-based anticancer drugs. In this perspective we highlight compounds that are apparently incompatible with the more classical (platinum-derived) concepts employed in the development of metal-based anticancer drugs, with respect to both compound design and the approaches used to validate their utility. Possible design approaches for the future are also suggested.
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Affiliation(s)
- Claire S Allardyce
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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290
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Clark AM, Dole K, Ekins S. Open Source Bayesian Models. 3. Composite Models for Prediction of Binned Responses. J Chem Inf Model 2016; 56:275-85. [PMID: 26750305 PMCID: PMC4764945 DOI: 10.1021/acs.jcim.5b00555] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Bayesian models constructed from
structure-derived fingerprints
have been a popular and useful method for drug discovery research
when applied to bioactivity measurements that can be effectively classified
as active or inactive. The results can be used to rank candidate structures
according to their probability of activity, and this ranking benefits
from the high degree of interpretability when structure-based fingerprints
are used, making the results chemically intuitive. Besides selecting
an activity threshold, building a Bayesian model is fast and requires
few or no parameters or user intervention. The method also does not
suffer from such acute overtraining problems as quantitative structure–activity
relationships or quantitative structure–property relationships
(QSAR/QSPR). This makes it an approach highly suitable for automated
workflows that are independent of user expertise or prior knowledge
of the training data. We now describe a new method for creating a
composite group of Bayesian models to extend the method to work with
multiple states, rather than just binary. Incoming activities are
divided into bins, each covering a mutually exclusive range of activities.
For each of these bins, a Bayesian model is created to model whether
or not the compound belongs in the bin. Analyzing putative molecules
using the composite model involves making a prediction for each bin
and examining the relative likelihood for each assignment, for example,
highest value wins. The method has been evaluated on a collection
of hundreds of data sets extracted from ChEMBL v20 and validated data
sets for ADME/Tox and bioactivity.
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Affiliation(s)
- Alex M Clark
- Molecular Materials Informatics, Inc. , 1900 St. Jacques #302, Montreal H3J 2S1, Quebec, Canada
| | - Krishna Dole
- Collaborative Drug Discovery, Inc. , 1633 Bayshore Highway, Suite 342, Burlingame, California 94010, United States
| | - Sean Ekins
- Collaborative Drug Discovery, Inc. , 1633 Bayshore Highway, Suite 342, Burlingame, California 94010, United States.,Collaborations in Chemistry , 5616 Hilltop Needmore Road, Fuquay-Varina, North Carolina 27526, United States
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291
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Wang L, Chen L, Yu M, Xu LH, Cheng B, Lin YS, Gu Q, He XH, Xu J. Discovering new mTOR inhibitors for cancer treatment through virtual screening methods and in vitro assays. Sci Rep 2016; 6:18987. [PMID: 26732172 PMCID: PMC4702177 DOI: 10.1038/srep18987] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 11/27/2015] [Indexed: 12/31/2022] Open
Abstract
Mammalian target of rapamycin (mTOR) is an attractive target for new anticancer drug development. We recently developed in silico models to distinguish mTOR inhibitors and non-inhibitors. In this study, we developed an integrated strategy for identifying new mTOR inhibitors using cascaded in silico screening models. With this strategy, fifteen new mTOR kinase inhibitors including four compounds with IC50 values below 10 μM were discovered. In particular, compound 17 exhibited potent anticancer activities against four tumor cell lines, including MCF-7, HeLa, MGC-803, and C6, with IC50 values of 1.90, 2.74, 3.50 and 11.05 μM. Furthermore, cellular studies and western blot analyses revealed that 17 induces cell death via apoptosis by targeting both mTORC1 and mTORC2 within cells and arrests the cell cycle of HeLa at the G1/G0-phase. Finally, multi-nanosecond explicit solvent simulations and MM/GBSA analyses were carried out to study the inhibitory mechanisms of 13, 17, and 40 for mTOR. The potent compounds presented here are worthy of further investigation.
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Affiliation(s)
- Ling Wang
- Research Center for Drug Discovery &Institute of Human Virology, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China.,Pre-Incubator for Innovative Drugs &Medicine, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Lei Chen
- Research Center for Drug Discovery &Institute of Human Virology, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Miao Yu
- Research Center for Drug Discovery &Institute of Human Virology, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Li-Hui Xu
- Department of Cell Biology, Jinan University, Guangzhou, 510632, China
| | - Bao Cheng
- Research Center for Drug Discovery &Institute of Human Virology, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Yong-Sheng Lin
- Research Center for Drug Discovery &Institute of Human Virology, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Qiong Gu
- Research Center for Drug Discovery &Institute of Human Virology, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Xian-Hui He
- Department of Immunobiology, Jinan University, Guangzhou, 510632, China
| | - Jun Xu
- Research Center for Drug Discovery &Institute of Human Virology, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
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292
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Glaser J, Holzgrabe U. Focus on PAINS: false friends in the quest for selective anti-protozoal lead structures from Nature? MEDCHEMCOMM 2016. [DOI: 10.1039/c5md00481k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Pan-assay interference compounds (PAINS) are molecules showing promising but deceptive activities in various biochemical screenings mainly due to unselective interactions with the target.
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Affiliation(s)
- J. Glaser
- Institute of Pharmacy and Food Chemistry
- University of Wuerzburg
- 97074 Wuerzburg
- Germany
| | - U. Holzgrabe
- Institute of Pharmacy and Food Chemistry
- University of Wuerzburg
- 97074 Wuerzburg
- Germany
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293
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Du X, Zhou J, Shi J, Xu B. Supramolecular Hydrogelators and Hydrogels: From Soft Matter to Molecular Biomaterials. Chem Rev 2015; 115:13165-307. [PMID: 26646318 PMCID: PMC4936198 DOI: 10.1021/acs.chemrev.5b00299] [Citation(s) in RCA: 1266] [Impact Index Per Article: 140.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Indexed: 12/19/2022]
Abstract
In this review we intend to provide a relatively comprehensive summary of the work of supramolecular hydrogelators after 2004 and to put emphasis particularly on the applications of supramolecular hydrogels/hydrogelators as molecular biomaterials. After a brief introduction of methods for generating supramolecular hydrogels, we discuss supramolecular hydrogelators on the basis of their categories, such as small organic molecules, coordination complexes, peptides, nucleobases, and saccharides. Following molecular design, we focus on various potential applications of supramolecular hydrogels as molecular biomaterials, classified by their applications in cell cultures, tissue engineering, cell behavior, imaging, and unique applications of hydrogelators. Particularly, we discuss the applications of supramolecular hydrogelators after they form supramolecular assemblies but prior to reaching the critical gelation concentration because this subject is less explored but may hold equally great promise for helping address fundamental questions about the mechanisms or the consequences of the self-assembly of molecules, including low molecular weight ones. Finally, we provide a perspective on supramolecular hydrogelators. We hope that this review will serve as an updated introduction and reference for researchers who are interested in exploring supramolecular hydrogelators as molecular biomaterials for addressing the societal needs at various frontiers.
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Affiliation(s)
- Xuewen Du
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Jie Zhou
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Junfeng Shi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
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294
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Hanson SM, Ekins S, Chodera JD. Modeling error in experimental assays using the bootstrap principle: understanding discrepancies between assays using different dispensing technologies. J Comput Aided Mol Des 2015; 29:1073-86. [PMID: 26678597 DOI: 10.1007/s10822-015-9888-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 12/07/2015] [Indexed: 11/26/2022]
Abstract
All experimental assay data contains error, but the magnitude, type, and primary origin of this error is often not obvious. Here, we describe a simple set of assay modeling techniques based on the bootstrap principle that allow sources of error and bias to be simulated and propagated into assay results. We demonstrate how deceptively simple operations--such as the creation of a dilution series with a robotic liquid handler--can significantly amplify imprecision and even contribute substantially to bias. To illustrate these techniques, we review an example of how the choice of dispensing technology can impact assay measurements, and show how large contributions to discrepancies between assays can be easily understood and potentially corrected for. These simple modeling techniques--illustrated with an accompanying IPython notebook--can allow modelers to understand the expected error and bias in experimental datasets, and even help experimentalists design assays to more effectively reach accuracy and imprecision goals.
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Affiliation(s)
- Sonya M Hanson
- Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Sean Ekins
- Collaborations in Chemistry, Fuquay-Varina, NC, 27526, USA
| | - John D Chodera
- Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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295
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Roberts JM, Bradner JE. A Bead-Based Proximity Assay for BRD4 Ligand Discovery. CURRENT PROTOCOLS IN CHEMICAL BIOLOGY 2015; 7:263-278. [PMID: 26629616 PMCID: PMC4725578 DOI: 10.1002/9780470559277.ch150024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bromodomain-containing proteins have emerged as desirable targets for anti-neoplastic and anti-inflammatory drug discovery. Toward the development of selective inhibitors of the BET family of bromodomains, we optimized bead-based assays to detect interactions between bromodomains and poly-acetylated histone peptides. Donor and acceptor beads bound to target and ligand are brought into proximity by this protein-protein interaction. After laser illumination, singlet oxygen evolved from donor beads travels to the spatially close acceptor beads, resulting in chemiluminesence. This AlphaScreen assay has proven amendable to high-throughput screening, secondary validation, and specificity profiling during lead discovery and optimization. Here we report our protocol for assay development to measure inhibition of ligand binding to bromodomain-containing protein 4 (BRD4). We discuss the discovery of an appropriate probe, optimization of bead, probe, and protein concentrations, and the derivation of protein-probe inhibition curves. Finally, we explore the implementation of this technology for high-throughput screening of potential BRD4 inhibitors.
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Affiliation(s)
- Justin M. Roberts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, Massachusetts 02215, USA
| | - James E. Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, Massachusetts 02215, USA
- Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA
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296
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Linke P, Amaning K, Maschberger M, Vallee F, Steier V, Baaske P, Duhr S, Breitsprecher D, Rak A. An Automated Microscale Thermophoresis Screening Approach for Fragment-Based Lead Discovery. ACTA ACUST UNITED AC 2015; 21:414-21. [PMID: 26637553 PMCID: PMC4800460 DOI: 10.1177/1087057115618347] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/28/2015] [Indexed: 11/17/2022]
Abstract
Fragment-based lead discovery has proved to be an effective alternative to high-throughput screenings in identifying chemical matter that can be developed into robust lead compounds. The search for optimal combinations of biophysical techniques that can correctly and efficiently identify and quantify binding can be challenging due to the physicochemical properties of fragments. In order to minimize the time and costs of screening, optimal combinations of biophysical techniques with maximal information content, sensitivity, and robustness are needed. Here we describe an approach utilizing automated microscale thermophoresis (MST) affinity screening to identify fragments active against MEK1 kinase. MST identified multiple hits that were confirmed by X-ray crystallography but not detected by orthogonal methods. Furthermore, MST also provided information about ligand-induced aggregation and protein denaturation. The technique delivered a large number of binders while reducing experimentation time and sample consumption, demonstrating the potential of MST to execute and maximize the efficacy of fragment screening campaigns.
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Affiliation(s)
- Pawel Linke
- NanoTemper Technologies GmbH, Munich, Germany
| | - Kwame Amaning
- Sanofi R&D, Structure-Design-Informatics, Vitry sur Seine, France
| | | | - Francois Vallee
- Sanofi R&D, Structure-Design-Informatics, Vitry sur Seine, France
| | - Valerie Steier
- Sanofi R&D, Structure-Design-Informatics, Vitry sur Seine, France
| | | | - Stefan Duhr
- NanoTemper Technologies GmbH, Munich, Germany
| | | | - Alexey Rak
- Sanofi R&D, Structure-Design-Informatics, Vitry sur Seine, France
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297
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Prade E, Bittner HJ, Sarkar R, Lopez Del Amo JM, Althoff-Ospelt G, Multhaup G, Hildebrand PW, Reif B. Structural Mechanism of the Interaction of Alzheimer Disease Aβ Fibrils with the Non-steroidal Anti-inflammatory Drug (NSAID) Sulindac Sulfide. J Biol Chem 2015; 290:28737-45. [PMID: 26416887 PMCID: PMC4661391 DOI: 10.1074/jbc.m115.675215] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 09/14/2015] [Indexed: 01/12/2023] Open
Abstract
Alzheimer disease is the most severe neurodegenerative disease worldwide. In the past years, a plethora of small molecules interfering with amyloid-β (Aβ) aggregation has been reported. However, their mode of interaction with amyloid fibers is not understood. Non-steroidal anti-inflammatory drugs (NSAIDs) are known γ-secretase modulators; they influence Aβ populations. It has been suggested that NSAIDs are pleiotrophic and can interact with more than one pathomechanism. Here we present a magic angle spinning solid-state NMR study demonstrating that the NSAID sulindac sulfide interacts specifically with Alzheimer disease Aβ fibrils. We find that sulindac sulfide does not induce drastic architectural changes in the fibrillar structure but intercalates between the two β-strands of the amyloid fibril and binds to hydrophobic cavities, which are found consistently in all analyzed structures. The characteristic Asp(23)-Lys(28) salt bridge is not affected upon interacting with sulindac sulfide. The primary binding site is located in the vicinity of residue Gly(33), a residue involved in Met(35) oxidation. The results presented here will assist the search for pharmacologically active molecules that can potentially be employed as lead structures to guide the design of small molecules for the treatment of Alzheimer disease.
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Affiliation(s)
- Elke Prade
- From the Munich Center for Integrated Protein Science at Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Heiko J Bittner
- Molecular Modeling, Institute of Medical Physics and Biophysics, Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Riddhiman Sarkar
- From the Munich Center for Integrated Protein Science at Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | | | | | - Gerd Multhaup
- the Department of Pharmacology and Therapeutics, McGill University, Montreal Quebec H3G 1Y6, Canada, and
| | - Peter W Hildebrand
- Molecular Modeling, Institute of Medical Physics and Biophysics, Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Bernd Reif
- From the Munich Center for Integrated Protein Science at Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany, the Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landtstr. 1, 85764 Neuherberg, Germany
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298
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Stone VN, Parikh HI, El-rami F, Ge X, Chen W, Zhang Y, Kellogg GE, Xu P. Identification of Small-Molecule Inhibitors against Meso-2, 6-Diaminopimelate Dehydrogenase from Porphyromonas gingivalis. PLoS One 2015; 10:e0141126. [PMID: 26544875 PMCID: PMC4636305 DOI: 10.1371/journal.pone.0141126] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/05/2015] [Indexed: 01/03/2023] Open
Abstract
Species-specific antimicrobial therapy has the potential to combat the increasing threat of antibiotic resistance and alteration of the human microbiome. We therefore set out to demonstrate the beginning of a pathogen-selective drug discovery method using the periodontal pathogen Porphyromonas gingivalis as a model. Through our knowledge of metabolic networks and essential genes we identified a “druggable” essential target, meso-diaminopimelate dehydrogenase, which is found in a limited number of species. We adopted a high-throughput virtual screen method on the ZINC chemical library to select a group of potential small-molecule inhibitors. Meso-diaminopimelate dehydrogenase from P. gingivalis was first expressed and purified in Escherichia coli then characterized for enzymatic inhibitor screening studies. Several inhibitors with similar structural scaffolds containing a sulfonamide core and aromatic substituents showed dose-dependent inhibition. These compounds were further assayed showing reasonable whole-cell activity and the inhibition mechanism was determined. We conclude that the establishment of this target and screening strategy provides a model for the future development of new antimicrobials.
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Affiliation(s)
- Victoria N. Stone
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Hardik I. Parikh
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Fadi El-rami
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Xiuchun Ge
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Weihau Chen
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Yan Zhang
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Glen E. Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Ping Xu
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
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299
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Matuszek AM, Reynisson J. Defining Known Drug Space Using DFT. Mol Inform 2015; 35:46-53. [DOI: 10.1002/minf.201500105] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 10/12/2015] [Indexed: 11/09/2022]
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300
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Dahlin JL, Nissink JWM, Francis S, Strasser JM, John K, Zhang Z, Walters MA. Post-HTS case report and structural alert: Promiscuous 4-aroyl-1,5-disubstituted-3-hydroxy-2H-pyrrol-2-one actives verified by ALARM NMR. Bioorg Med Chem Lett 2015; 25:4740-4752. [PMID: 26318992 PMCID: PMC6002837 DOI: 10.1016/j.bmcl.2015.08.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 07/29/2015] [Accepted: 08/06/2015] [Indexed: 12/19/2022]
Abstract
Despite its wide use, not every high-throughput screen (HTS) yields chemical matter suitable for drug development campaigns, and seldom are 'go/no-go' decisions in drug discovery described in detail. This case report describes the follow-up of a 4-aroyl-1,5-disubstituted-3-hydroxy-2H-pyrrol-2-one active from a cell-free HTS to identify small-molecule inhibitors of Rtt109-catalyzed histone acetylation. While this compound and structural analogs inhibited Rtt109-catalyzed histone acetylation in vitro, further work on this series was halted after several risk mitigation strategies were performed. Compounds with this chemotype had a poor structure-activity relationship, exhibited poor selectivity among other histone acetyltransferases, and tested positive in a β-lactamase counter-screen for chemical aggregates. Furthermore, ALARM NMR demonstrated compounds with this chemotype grossly perturbed the conformation of the La protein. In retrospect, this chemotype was flagged as a 'frequent hitter' in an analysis of a large corporate screening deck, yet similar compounds have been published as screening actives or chemical probes versus unrelated biological targets. This report-including the decision-making process behind the 'no-go' decision-should be informative for groups engaged in post-HTS triage and highlight the importance of considering physicochemical properties in early drug discovery.
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Affiliation(s)
- Jayme L Dahlin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA; Medical Scientist Training Program, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | | | - Subhashree Francis
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55414, USA
| | - Jessica M Strasser
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55414, USA
| | - Kristen John
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55414, USA
| | - Zhiguo Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Michael A Walters
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55414, USA.
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