1
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Charest N, Lowe CN, Ramsland C, Meyer B, Samano V, Williams AJ. Improving predictions of compound amenability for liquid chromatography-mass spectrometry to enhance non-targeted analysis. Anal Bioanal Chem 2024:10.1007/s00216-024-05229-5. [PMID: 38530399 DOI: 10.1007/s00216-024-05229-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/28/2024]
Abstract
Mass-spectrometry-based non-targeted analysis (NTA), in which mass spectrometric signals are assigned chemical identities based on a systematic collation of evidence, is a growing area of interest for toxicological risk assessment. Successful NTA results in better identification of potentially hazardous pollutants within the environment, facilitating the development of targeted analytical strategies to best characterize risks to human and ecological health. A supporting component of the NTA process involves assessing whether suspected chemicals are amenable to the mass spectrometric method, which is necessary in order to assign an observed signal to the chemical structure. Prior work from this group involved the development of a random forest model for predicting the amenability of 5517 unique chemical structures to liquid chromatography-mass spectrometry (LC-MS). This work improves the interpretability of the group's prior model of the same endpoint, as well as integrating 1348 more data points across negative and positive ionization modes. We enhance interpretability by feature engineering, a machine learning practice that reduces the input dimensionality while attempting to preserve performance statistics. We emphasize the importance of interpretable machine learning models within the context of building confidence in NTA identification. The novel data were curated by the labeling of compounds as amenable or unamenable by expert curators, resulting in an enhanced set of chemical compounds to expand the applicability domain of the prior model. The balanced accuracy benchmark of the newly developed model is comparable to performance previously reported (mean CV BA is 0.84 vs. 0.82 in positive mode, and 0.85 vs. 0.82 in negative mode), while on a novel external set, derived from this work's data, the Matthews correlation coefficients (MCC) for the novel models are 0.66 and 0.68 for positive and negative mode, respectively. Our group's prior published models scored MCC of 0.55 and 0.54 on the same external sets. This demonstrates appreciable improvement over the chemical space captured by the expanded dataset. This work forms part of our ongoing efforts to develop models with higher interpretability and higher performance to support NTA efforts.
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Affiliation(s)
- Nathaniel Charest
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, 27711, USA.
| | - Charles N Lowe
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, 27711, USA
| | | | - Brian Meyer
- Senior Environmental Employment Program, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, 27711, USA
| | - Vicente Samano
- Senior Environmental Employment Program, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, 27711, USA
| | - Antony J Williams
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, 27711, USA
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2
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Sinclair G, Thillainadarajah I, Meyer B, Samano V, Sivasupramaniam S, Adams L, Willighagen EL, Richard AM, Walker M, Williams AJ. Wikipedia on the CompTox Chemicals Dashboard: Connecting Resources to Enrich Public Chemical Data. J Chem Inf Model 2022; 62:4888-4905. [PMID: 36215146 PMCID: PMC9597659 DOI: 10.1021/acs.jcim.2c00886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The online encyclopedia
Wikipedia aggregates a large amount of
data on chemistry, encompassing well over 20,000 individual Wikipedia
pages and serves the general public as well as the chemistry community.
Many other chemical databases and services utilize these data, and
previous projects have focused on methods to index, search, and extract
it for review and use. We present a comprehensive effort that combines
bulk automated data extraction over tens of thousands of pages, semiautomated
data extraction over hundreds of pages, and fine-grained manual extraction
of individual lists and compounds of interest. We then correlate these
data with the existing contents of the U.S. Environmental Protection
Agency’s (EPA) Distributed Structure-Searchable Toxicity (DSSTox)
database. This was performed with a number of intentions including
ensuring as complete a mapping as possible between the Dashboard and
Wikipedia so that relevant snippets of the article are loaded for
the user to review. Conflicts between Dashboard content and Wikipedia
in terms of, for example, identifiers such as chemical registry numbers,
names, and InChIs and structure-based collisions such as SMILES were
identified and used as the basis of curation of both DSSTox and Wikipedia.
This work also allowed us to evaluate available data for sets of chemicals
of interest to the Agency, such as synthetic cannabinoids, and expand
the content in DSSTox as appropriate. This work also led to improved
bidirectional linkage of the detailed chemistry and usage information
from Wikipedia with expert-curated structure and identifier data from
DSSTox for a new list of nearly 20,000 chemicals. All of this work
ultimately enhances the data mappings that allow for the display of
the introduction of the Wikipedia article in the community-accessible
web-based EPA Comptox Chemicals Dashboard, enhancing the user experience
for the thousands of users per day accessing the resource.
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Affiliation(s)
- Gabriel Sinclair
- ORAU Student Services Contractor to Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Inthirany Thillainadarajah
- Senior Environmental Employment Program, US Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Brian Meyer
- Senior Environmental Employment Program, US Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Vicente Samano
- Senior Environmental Employment Program, US Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Sakuntala Sivasupramaniam
- Senior Environmental Employment Program, US Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Linda Adams
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Egon L Willighagen
- Department of Bioinformatics─BiGCaT, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Ann M Richard
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Martin Walker
- Martin Walker, SUNY Potsdam─Chemistry, 44 Pierrepont Avenue, Potsdam, New York 13676, United States
| | - Antony J Williams
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
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3
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Williams AJ, Gaines LGT, Grulke CM, Lowe CN, Sinclair GFB, Samano V, Thillainadarajah I, Meyer B, Patlewicz G, Richard AM. Assembly and Curation of Lists of Per- and Polyfluoroalkyl Substances (PFAS) to Support Environmental Science Research. Front Environ Sci 2022; 10:1-13. [PMID: 35936994 PMCID: PMC9350880 DOI: 10.3389/fenvs.2022.850019] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are a class of man-made chemicals of global concern for many health and regulatory agencies due to their widespread use and persistence in the environment (in soil, air, and water), bioaccumulation, and toxicity. This concern has catalyzed a need to aggregate data to support research efforts that can, in turn, inform regulatory and statutory actions. An ongoing challenge regarding PFAS has been the shifting definition of what qualifies a substance to be a member of the PFAS class. There is no single definition for a PFAS, but various attempts have been made to utilize substructural definitions that either encompass broad working scopes or satisfy narrower regulatory guidelines. Depending on the size and specificity of PFAS substructural filters applied to the U.S. Environmental Protection Agency (EPA) DSSTox database, currently exceeding 900,000 unique substances, PFAS substructure-defined space can span hundreds to tens of thousands of compounds. This manuscript reports on the curation of PFAS chemicals and assembly of lists that have been made publicly available to the community via the EPA's CompTox Chemicals Dashboard. Creation of these PFAS lists required the harvesting of data from EPA and online databases, peer-reviewed publications, and regulatory documents. These data have been extracted and manually curated, annotated with structures, and made available to the community in the form of lists defined by structure filters, as well as lists comprising non-structurable PFAS, such as polymers and complex mixtures. These lists, along with their associated linkages to predicted and measured data, are fueling PFAS research efforts within the EPA and are serving as a valuable resource to the international scientific community.
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Affiliation(s)
- Antony J. Williams
- Office of Research & Development, Center for Computational Toxicology & Exposure, U.S. Environmental Protection Agency, Durham, NC, United States
| | - Linda G. T. Gaines
- Office of Land and Emergency Management, US Environmental Protection Agency, Washington, DC, United States
| | - Christopher M. Grulke
- Office of Research & Development, Center for Computational Toxicology & Exposure, U.S. Environmental Protection Agency, Durham, NC, United States
| | - Charles N. Lowe
- Office of Research & Development, Center for Computational Toxicology & Exposure, U.S. Environmental Protection Agency, Durham, NC, United States
| | - Gabriel F. B. Sinclair
- ORAU Student Services Contractor to U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology & Exposure, Oak Ridge, NC, United States
| | - Vicente Samano
- Senior Environmental Employment Program, US Environmental Protection Agency, Research Triangle Park, NC, United States
| | - Inthirany Thillainadarajah
- Senior Environmental Employment Program, US Environmental Protection Agency, Research Triangle Park, NC, United States
| | - Bryan Meyer
- Senior Environmental Employment Program, US Environmental Protection Agency, Research Triangle Park, NC, United States
| | - Grace Patlewicz
- Office of Research & Development, Center for Computational Toxicology & Exposure, U.S. Environmental Protection Agency, Durham, NC, United States
| | - Ann M. Richard
- Office of Research & Development, Center for Computational Toxicology & Exposure, U.S. Environmental Protection Agency, Durham, NC, United States
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4
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Kazmierski WM, Xia B, Miller J, De la Rosa M, Favre D, Dunham RM, Washio Y, Zhu Z, Wang F, Mebrahtu M, Deng H, Basilla J, Wang L, Evindar G, Fan L, Olszewski A, Prabhu N, Davie C, Messer JA, Samano V. DNA-Encoded Library Technology-Based Discovery, Lead Optimization, and Prodrug Strategy toward Structurally Unique Indoleamine 2,3-Dioxygenase-1 (IDO1) Inhibitors. J Med Chem 2020; 63:3552-3562. [PMID: 32073266 DOI: 10.1021/acs.jmedchem.9b01799] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report the discovery of a novel indoleamine 2,3-dioxygenase-1 (IDO1) inhibitor class through the affinity selection of a previously unreported indole-based DNA-encoded library (DEL). The DEL exemplar, spiro-chromane 1, had moderate IDO1 potency but high in vivo clearance. Series optimization quickly afforded a potent, low in vivo clearance lead 11. Although amorphous 11 was highly bio-available, crystalline 11 was poorly soluble and suffered disappointingly low bio-availability because of solubility-limited absorption. A prodrug approach was deployed and proved effective in discovering the highly bio-available phosphonooxymethyl 31, which rapidly converted to 11 in vivo. Obtaining crystalline 31 proved problematic, however; thus salt screening was performed in an attempt to circumvent this obstacle and successfully delivered greatly soluble and bio-available crystalline tris-salt 32. IDO1 inhibitor 32 is characterized by a low calculated human dose, best-in-class potential, and an unusual inhibition mode by binding the IDO1 heme-free (apo) form.
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Affiliation(s)
- Wieslaw M Kazmierski
- HIV Discovery Performance Unit, GlaxoSmithKline, Research Triangle Park, Durham, North Carolina 27709, United States
| | - Bing Xia
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - John Miller
- HIV Discovery Performance Unit, GlaxoSmithKline, Research Triangle Park, Durham, North Carolina 27709, United States
| | - Martha De la Rosa
- HIV Discovery Performance Unit, GlaxoSmithKline, Research Triangle Park, Durham, North Carolina 27709, United States
| | - David Favre
- HIV Discovery Performance Unit, GlaxoSmithKline, Research Triangle Park, Durham, North Carolina 27709, United States
| | - Richard M Dunham
- HIV Discovery Performance Unit, GlaxoSmithKline, Research Triangle Park, Durham, North Carolina 27709, United States
| | - Yoshiaki Washio
- MST Medicine Design, Medicinal Chemistry, GlaxoSmithKline, Gunnels Wood Rd, Stevenage SG1 2NY, U.K
| | - Zhengrong Zhu
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Feng Wang
- DMPK/IVIVT, GlaxoSmithKline, 1250 S. Collegeville Rd, Collegeville, Pennsylvania 19426-0989, United States
| | - Makda Mebrahtu
- Screening, Profiling & Mechanistic Biology, RD Platform Technology & Science, GlaxoSmithKline, 1250 S. Collegeville Rd, Collegeville, Pennsylvania 19426-0989, United States
| | - Hongfeng Deng
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Jonathan Basilla
- Screening, Profiling & Mechanistic Biology, RD Platform Technology & Science, GlaxoSmithKline, 1250 S. Collegeville Rd, Collegeville, Pennsylvania 19426-0989, United States
| | - Liping Wang
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Rd, Collegeville, Pennsylvania 19426, United States
| | - Ghotas Evindar
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Lijun Fan
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Alison Olszewski
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Ninad Prabhu
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Christopher Davie
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Jeffrey A Messer
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Vicente Samano
- HIV Discovery Performance Unit, GlaxoSmithKline, Research Triangle Park, Durham, North Carolina 27709, United States
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5
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Maynard A, Crosby RM, Ellis B, Hamatake R, Hong Z, Johns BA, Kahler KM, Koble C, Leivers A, Leivers MR, Mathis A, Peat AJ, Pouliot JJ, Roberts CD, Samano V, Schmidt RM, Smith GK, Spaltenstein A, Stewart EL, Thommes P, Turner EM, Voitenleitner C, Walker JT, Waitt G, Weatherhead J, Weaver K, Williams S, Wright L, Xiong ZZ, Haigh D, Shotwell JB. Discovery of a Potent Boronic Acid Derived Inhibitor of the HCV RNA-Dependent RNA Polymerase. J Med Chem 2013; 57:1902-13. [DOI: 10.1021/jm400317w] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Andrew Maynard
- GlaxoSmithKline,
Platform Technology and Science, 5 Moore Drive, Research Triangle
Park, North Carolina 27709-3398, United States
| | - Renae M. Crosby
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Byron Ellis
- GlaxoSmithKline,
Platform Technology and Science, 5 Moore Drive, Research Triangle
Park, North Carolina 27709-3398, United States
| | - Robert Hamatake
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Zhi Hong
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Brian A. Johns
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Kirsten M. Kahler
- GlaxoSmithKline,
Platform Technology and Science, 5 Moore Drive, Research Triangle
Park, North Carolina 27709-3398, United States
| | - Cecilia Koble
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Anna Leivers
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Martin R. Leivers
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Amanda Mathis
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Andrew J. Peat
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Jeffrey J. Pouliot
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Christopher D. Roberts
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Vicente Samano
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Rachel M. Schmidt
- GlaxoSmithKline,
Platform Technology and Science, 5 Moore Drive, Research Triangle
Park, North Carolina 27709-3398, United States
| | - Gary K. Smith
- GlaxoSmithKline,
Platform Technology and Science, 5 Moore Drive, Research Triangle
Park, North Carolina 27709-3398, United States
| | - Andrew Spaltenstein
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Eugene L. Stewart
- GlaxoSmithKline,
Platform Technology and Science, 5 Moore Drive, Research Triangle
Park, North Carolina 27709-3398, United States
| | - Pia Thommes
- GlaxoSmithKline, Infectious Diseases Centre
for Excellence for Drug Discovery, Gunnels Wood Road, Stevenage, Hertfordshire
SG1 1NY, U.K
| | - Elizabeth M. Turner
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Christian Voitenleitner
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Jill T. Walker
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Greg Waitt
- GlaxoSmithKline,
Platform Technology and Science, 5 Moore Drive, Research Triangle
Park, North Carolina 27709-3398, United States
| | - Jason Weatherhead
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - Kurt Weaver
- GlaxoSmithKline,
Platform Technology and Science, 5 Moore Drive, Research Triangle
Park, North Carolina 27709-3398, United States
| | - Shawn Williams
- GlaxoSmithKline,
Platform Technology and Science, 5 Moore Drive, Research Triangle
Park, North Carolina 27709-3398, United States
| | - Lois Wright
- GlaxoSmithKline,
Platform Technology and Science, 5 Moore Drive, Research Triangle
Park, North Carolina 27709-3398, United States
| | - Zhiping Z. Xiong
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
| | - David Haigh
- GlaxoSmithKline, Infectious Diseases Centre
for Excellence for Drug Discovery, Gunnels Wood Road, Stevenage, Hertfordshire
SG1 1NY, U.K
| | - J. Brad Shotwell
- GlaxoSmithKline, Infectious Diseases Medicines Discovery Unit, 5
Moore Drive, Research Triangle Park, North Carolina 27709-3398, United
States
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6
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Smalley TL, Chamberlain SD, Mills WY, Musso DL, Randhawa SA, Ray JA, Samano V, Frick L. Synthesis of novel anilinoquinolines as c-fms inhibitors. Bioorg Med Chem Lett 2007; 17:6257-60. [PMID: 17870531 DOI: 10.1016/j.bmcl.2007.09.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2007] [Revised: 08/27/2007] [Accepted: 09/04/2007] [Indexed: 11/25/2022]
Abstract
A novel series of potent substituted anilinoquinolines were discovered as c-fms inhibitors. The potency could be manipulated upon modification of the C4 aniline and C7 aryl functionality. Pharmacokinetic analysis identified a metabolically stable analog suitable for further investigative work.
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Affiliation(s)
- Terrence L Smalley
- GlaxoSmithKline, Inc., Five Moore Drive, Research Triangle Park, NC 27709, USA.
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7
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Boggs SD, Cobb JD, Gudmundsson KS, Jones LA, Matsuoka RT, Millar A, Patterson DE, Samano V, Trone MD, Xie S, Zhou XM. Efficient Asymmetric Synthesis ofN-[(1R)-6-Chloro-2,3,4,9-tetrahydro-1H-carbazol-1-yl]-2-pyridinecarboxamide for Treatment of Human Papillomavirus Infections. Org Process Res Dev 2007. [DOI: 10.1021/op060223v] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Barrett DG, Catalano JG, Deaton DN, Long ST, McFadyen RB, Miller AB, Miller LR, Samano V, Tavares FX, Wells-Knecht KJ, Wright LL, Zhou HQQ. Acyclic, orally bioavailable ketone-based cathepsin K inhibitors. Bioorg Med Chem Lett 2006; 17:22-7. [PMID: 17157021 DOI: 10.1016/j.bmcl.2006.10.102] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Revised: 10/03/2006] [Accepted: 10/04/2006] [Indexed: 11/22/2022]
Abstract
Starting from a potent ketone-based inhibitor with poor drug properties, incorporation of P(2)-P(3) elements from a ketoamide-based inhibitor led to the identification of a hybrid series of ketone-based cathepsin K inhibitors with better oral bioavailability than the starting ketone.
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Affiliation(s)
- David G Barrett
- Department of Medicinal Chemistry, GlaxoSmithKline, Research Triangle Park, NC 27709, USA
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9
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McDonald O, Lackey K, Davis-Ward R, Wood E, Samano V, Maloney P, Deanda F, Hunter R. Aza-stilbenes as potent and selective c-RAF inhibitors. Bioorg Med Chem Lett 2006; 16:5378-83. [PMID: 16890436 DOI: 10.1016/j.bmcl.2006.07.063] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2006] [Revised: 07/19/2006] [Accepted: 07/21/2006] [Indexed: 10/24/2022]
Abstract
The synthesis of several novel aza-stilbene derivatives was carried out. The compounds were tested for their c-RAF enzyme inhibition. Compound 27 possesses significant potency against c-RAF and demonstrates selectivity over other protein kinases. A hypothesis for the binding mode, activity, and selectivity is proposed.
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10
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Barrett DG, Catalano JG, Deaton DN, Hassell AM, Long ST, Miller AB, Miller LR, Ray JA, Samano V, Shewchuk LM, Wells-Knecht KJ, Willard DH, Wright LL. Novel, potent P2–P3 pyrrolidine derivatives of ketoamide-based cathepsin K inhibitors. Bioorg Med Chem Lett 2006; 16:1735-9. [PMID: 16376075 DOI: 10.1016/j.bmcl.2005.11.101] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Revised: 11/29/2005] [Accepted: 11/30/2005] [Indexed: 10/25/2022]
Abstract
Starting from a potent pantolactone ketoamide cathepsin K inhibitor discovered from structural screening, conversion of the lactone scaffold to a pyrrolidine scaffold allowed exploration of the S(3) subsite of cathepsin K. Manipulation of P3 and P1' groups afforded potent inhibitors with drug-like properties.
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Affiliation(s)
- David G Barrett
- Department of Medicinal Chemistry, GlaxoSmithKline, Research Triangle Park, NC 27709, USA
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11
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Abstract
Due to factors such as resistance and long-term side effects as well as dosing regimen-related adherence issues, HIV therapy is a constantly moving target. HIV-1 protease inhibitors had an immediate and dramatic impact on the outcome of HIV/AIDS when launched in late 1995, and the search for new and improved next generation molecules has been under way in many laboratories. At GlaxoSmithKline (GSK) and Vertex Pharmaceuticals, this effort focused on two key issues, patient compliance and viral resistance. Using a water-solubilizing prodrug approach, the pill-burden in delivering our protease inhibitor, amprenavir, was dramatically decreased. By eliminating the large amounts of excipients necessary for the original soft-gel formulation, fosamprenavir (Lexiva/Telzir) delivers the clinically efficacious dose of amprenavir with two compact tablets per dose, compared to eight gel capsules. Our efforts to overcome viral resistance to 1(st) generation protease inhibitors by further elaborating the SAR of the amprenavir and related scaffolds, led to successive and dramatic improvements in wild-type antiviral potencies, and ultimately to the discovery of "ultra-potent" molecules with very favorable overall resistance profiles. The selection of GW640385 (brecanvir--USAN approved only) as a clinical candidate and its progression into current phase 2 dose ranging studies represents the culmination of our effort toward next generation protease inhibitors.
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Affiliation(s)
- Andrew Spaltenstein
- Division of Chemistry, MV CEDD, GlaxoSmithKline, 2512 S. Tricenter Boulevard, Research Triangle Park, NC 27709, USA.
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12
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Barrett DG, Boncek VM, Catalano JG, Deaton DN, Hassell AM, Jurgensen CH, Long ST, McFadyen RB, Miller AB, Miller LR, Payne JA, Ray JA, Samano V, Shewchuk LM, Tavares FX, Wells-Knecht KJ, Willard DH, Wright LL, Zhou HQQ. P2-P3 conformationally constrained ketoamide-based inhibitors of cathepsin K. Bioorg Med Chem Lett 2005; 15:3540-6. [PMID: 15982880 DOI: 10.1016/j.bmcl.2005.05.062] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2005] [Revised: 05/16/2005] [Accepted: 05/17/2005] [Indexed: 11/15/2022]
Abstract
An orally bioavailable series of ketoamide-based cathepsin K inhibitors with good pharmacokinetic properties has been identified. Starting from a potent inhibitor endowed with poor drug properties, conformational constraint of the P(2)-P(3) linker and modifications to P(1') elements led to an enhancement in potency, solubility, clearance, and bioavailability. These optimized inhibitors attenuated bone resorption in a rat TPTX hypocalcemic bone resorption model.
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Affiliation(s)
- David G Barrett
- Department of Medicinal Chemistry, GlaxoSmithKline, Research Triangle Park, NC 27709, USA
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13
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Savarese JJ, Belmont MR, Hashim MA, Mook RA, Boros EE, Samano V, Patel SS, Feldman PL, Schultz JAI, McNulty M, Spitzer T, Cohn DL, Morgan P, Wastila WB. Preclinical Pharmacology of GW280430A (AV430A) in the Rhesus Monkey and in the Cat. Anesthesiology 2004; 100:835-45. [PMID: 15087618 DOI: 10.1097/00000542-200404000-00013] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Background
No replacement for succinylcholine is yet available. GW280430A (AV430A) is a representative of a new class of nondepolarizing neuromuscular blocking drugs called asymmetric mixed-onium chlorofumarates. It undergoes rapid degradation in plasma by chemical hydrolysis and inactivation by cysteine adduction, resulting in a very short duration of effect. The neuromuscular, cardiovascular, and autonomic pharmacology of GW280430A is compared herein with that of mivacurium.
Methods
Adult male rhesus monkeys and adult male cats were anesthetized with nitrous oxide-oxygen-halothane and chloralose-pentobarbital, respectively. The neuromuscular blocking properties of GW280430A and mivacurium were compared at a stimulation rate of 0.15 Hz in the extensor digitorum of the foot (monkey) and the tibialis anterior (cat). Sympathetic responses were assayed in the cat in the nictitating membrane preparation, and vagal effects were evaluated in the cat via observation of bradycardic responses after stimulation of the cervical right vagus nerve.
Results
GW280430A and mivacurium were equipotent in the monkey (ED95 was 0.06 mg/kg in each case). GW280430A was half as potent as mivacurium in the cat. The total duration of action of GW280430A was less than half that of mivacurium in the monkey; recovery slopes were more than twice as rapid. The 25-75% recovery index of GW280430A did not vary significantly after various bolus doses or infusions, averaging 1.4-1.8 min in the monkey, significantly shorter than the same time interval (4.8-5.7 min) for mivacurium. Dose ratios for autonomic versus neuromuscular blocking properties in the cat were greater than 25 for both GW280430A and mivacurium. The ratio ED Hist:ED95 Neuromuscular Block in the monkey was significantly greater (approximately 53 vs. 13) for GW280430A, indicating approximately four times less relative prominence of the side effects of skin flushing and decrease of blood pressure, which are associated with release of histamine.
Conclusions
These experiments show a much shorter neuromuscular blocking effect and much-reduced side effects in the case of GW280430A vis-à-vis mivacurium. These results, together with the novel chemical degradation of GW280430A, suggest further evaluation in human subjects.
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Affiliation(s)
- John J Savarese
- Department of Anesthesiology, Weill Medical College of Cornell University and New York-Presbyterian Hospital, New York, New York 10021, USA.
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14
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Miller JF, Furfine ES, Hanlon MH, Hazen RJ, Ray JA, Robinson L, Samano V, Spaltenstein A. Novel arylsulfonamides possessing sub-picomolar HIV protease activities and potent anti-HIV activity against wild-type and drug-resistant viral strains. Bioorg Med Chem Lett 2004; 14:959-63. [PMID: 15013001 DOI: 10.1016/j.bmcl.2003.12.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2003] [Revised: 11/24/2003] [Accepted: 12/02/2003] [Indexed: 10/26/2022]
Abstract
A novel series of P1' chain-extended arylsufonamides was synthesized and evaluated for wild-type HIV protease inhibitory activity and in vitro antiviral activity against wild type virus and two protease inhibitor-resistant mutant viruses. All of the compounds showed dramatic increases in enzyme activity as compared to the currently marketed HIV protease inhibitors amprenavir, indinavir, and nelfinavir. In addition, significant improvements in antiviral potencies against wild type and the two mutant viruses were also realized.
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Affiliation(s)
- John F Miller
- GlaxoSmithKline, 5 Moore Drive, Research Triangle Park, NC 27709, USA.
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15
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Boros EE, Samano V, Ray JA, Thompson JB, Jung DK, Kaldor I, Koble CS, Martin MT, Styles VL, Mook RA, Feldman PL, Savarese JJ, Belmont MR, Bigham EC, Boswell GE, Hashim MA, Patel SS, Wisowaty JC, Bowers GD, Moseley CL, Walsh JS, Reese MJ, Rutkowske RD, Sefler AM, Spitzer TD. Neuromuscular blocking activity and therapeutic potential of mixed-tetrahydroisoquinolinium halofumarates and halosuccinates in rhesus monkeys. J Med Chem 2003; 46:2502-15. [PMID: 12773054 DOI: 10.1021/jm020574+] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Structure-activity relationships in rhesus monkeys for a novel mixed-onium class of ultra-short-acting nondepolarizing tetrahydroisoquinolinium neuromuscular blockers (NMBs) are described. Bis-onium chlorofumarate 20a with (1R,2S)-benzyltetrahydroisoquinolinium groups was a potent lead compound (ED(95) = 0.079 mg/kg) with an ultra-short duration of NMB effect (7.1 min) and a selectivity index (SI: defined as a ratio of the cardiovascular threshold dose to the ED(95)) similar to that of mivacurium (3). The mean threshold dose for cardiovascular effects with 20a was ca. 20 times its ED(95) value (SI = 20). A novel mixed-onium analogue of 20a was prepared by replacing the benzyltetrahydroisoquinolinium group distal to the fumarate chlorine atom with a (1S,2R)-phenyltetrahydroisoquinolinium moiety. The resulting mixed-onium chlorofumarate 24a displayed good NMB potency (ED(95) = 0.063 mg/kg), ultra-short duration of action (5.6 min) and an improved selectivity index (SI = 57). Several other mixed-onium derivatives containing octanedioate (25a; ED(95) = 0.103 mg/kg), difluorosuccinate (27c; ED(95) = 0.056 mg/kg), and fluorofumarate (28a; ED(95) = 0.137 mg/kg) linkers were also potent, ultra-short-acting NMBs with good to excellent selectivity index values (SI = 37-96). Octanedioate 25a was longer acting at higher doses compared to difluorosuccinate 27c and chlorofumarate 24a. Durations of NMB effect following a 0.4 mg/kg bolus dose (100% block) of 25a, 27c, and 24a were 16.9, 13.0, and 10.0 min, respectively. Recovery time for mixed-onium chlorofumarate 24a following a 1 h continuous infusion at 10-20 microg/kg/min (95-100% block) was ca. 5 min which is similar to that observed following a 0.2 mg/kg bolus dose of this compound and indicates a lack of cummulative effects. Preliminary studies with chlorofumarate 24a in whole human blood revealed that mixed-onium thiazolidine 29 was the major metabolite and that plasma cholinesterases do not play the primary role in duration of NMB effect. The NMB properties of 24a in rhesus monkeys led to its clinical evaluation as a possible alternative to succinylcholine.
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Affiliation(s)
- Eric E Boros
- GlaxoSmithKline Research & Development, Five Moore Drive, Research Triangle Park, North Carolina 27709, USA.
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16
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Samano V, Miles RW, Robins MJ. Efficient Conversion of 6-Aminopurines and Nucleosides into 6-Substituted Analogs via Novel 6-(1,2,4-Triazol-4-yl)purine Derivatives. J Am Chem Soc 2002. [DOI: 10.1021/ja00099a061] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Samano V, Robins MJ. Nucleic acid and related compounds. 75. Synthesis and radical-induced ring-opening reactions of 2'-deoxyadenosine-2'-spirocyclopropane and its uridine analogs. Mechanistic probes for ribonucleotide reductases. J Am Chem Soc 2002. [DOI: 10.1021/ja00036a077] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Robins MJ, Samano V, Johnson MD. Nucleic acid-related compounds. 58. Periodinane oxidation, selective primary deprotection, and remarkably stereoselective reduction of tert-butyldimethylsilyl-protected ribonucleosides. Synthesis of 9-(.beta.-D-xylofuranosyl)adenine or 3'-deuterioadenosine from adenosine. J Org Chem 2002. [DOI: 10.1021/jo00289a004] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Miles RW, Samano V, Robins MJ. Nucleic Acid Related Compounds. 86. Nucleophilic Functionalization of Adenine, Adenosine, Tubercidin, and Formycin Derivatives via Elaboration of the Heterocyclic Amino Group into a Readily Displaced 1,2,4-Triazol-4-yl Substituent. J Am Chem Soc 2002. [DOI: 10.1021/ja00127a007] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Miles RW, Samano V, Robins MJ. Nucleic Acid Related Compounds. 87. Nucleophilic Functionalization of Cytidine and 2'-Deoxycytidine Derivatives via Elaboration of the 4-Amino Group into a Readily Displaced 1,2,4-Triazol-4-yl Substituent. J Org Chem 2002. [DOI: 10.1021/jo00126a078] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Fleming SA, Rawlins DB, Samano V, Robins MJ. Photochemistry of nucleoside transport inhibitor 6-S-benzylated thiopurine ribonucleosides. Implications for a new class of photoaffinity labels. J Org Chem 2002. [DOI: 10.1021/jo00048a034] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Samano V, Robins MJ. Nucleic acid related compounds. 60. Mild periodinane oxidation of protected nucleosides to give 2'- and 3'-ketonucleosides. The first isolation of a purine 2'-deoxy-3'-ketonucleoside derivative. J Org Chem 2002. [DOI: 10.1021/jo00305a003] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Samano V, Robins MJ. Nucleic acid related compounds. 70. Synthesis of 2'(and 3')-deoxy-2'(and 3')-methyleneadenosines and bis(methylene)furan 4',5'-didehydro-5'-deoxy-2'(and 3')-methyleneadenosines. Inhibitors of S-adenosyl-L-homocysteine hydrolase and ribonucleotide reductase. J Org Chem 2002. [DOI: 10.1021/jo00025a029] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Kaldor I, Feldman PL, Mook RA, Ray JA, Samano V, Sefler AM, Thompson JB, Travis BR, Boros EE. Stereocontrolled Synthesis of cis-Dibenzoquinolizine Chlorofumarates: Curare-Like Agents of Ultrashort Duration. J Org Chem 2001; 66:3495-501. [PMID: 11348135 DOI: 10.1021/jo010032k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The quaternizations of dibenzoquinolizines 9 and 14 with 3-halo-1-propanols are highly cis-selective (94-100% cis), results consistent with the N-methylation of O-methylcapaurine (7b), but in contrast to the proposed trans-stereochemistry of dibenzo[a,h]quinolizine methiodide 10 and the analogous quaternizations of 1-benzyl- and 1-phenylisoquinoline congeners 5b and 5c. In this report, we describe stereoselective preparation of the unique cis-dibenzoquinolizinium propanols 15 and 16and their transformation into bis- and mixed-onium chlorofumarates 19, 20ab, and 26. Dibenzo[a,g]quinolizinium propanol 15 was prepared enantioselectively in three steps from dihydroisoquinoline 11. Asymmetric transfer hydrogenation of 11 in the presence of triethylamine/formic acid and Noyori's chiral ruthenium catalyst 12 produced R-(-)-5',8-dimethoxynorlaudanosine (13) in 98% yield and 87% ee. Pictet-Spengler cyclization of 13 in formalin/formic acid afforded the dibenzo[a,g]quinolizine 14 in 65% yield. Quaternization of 14 with 3-chloro-1-propanol under Finkelstein conditions generated cis-dibenzoquinolizinium propanol 15 in 85% yield with >94% cis-selectivity. The cis-dibenzo[a,h]quinolizinium propanol 16 was obtained as a single stereoisomer by reaction of the known tetramethoxyquinolizine 9 with neat 3-iodo-1-propanol. Bis-onium chlorofumarates 18 and 19 and the mixed-onium derivative 20ab were prepared by a pool synthesis procedure from (1R)-trans-6a, 16, and chlorofumaryl chloride (17). Mixed-onium alpha-chlorofumarate 26 was synthesized from (1S)-trans-6d, 15 and (+/-)-trans-2,3-dichlorosuccinic anhydride (22), employing a recently disclosed chlorofumarate mixed-diester synthesis. The title compounds (19, 20ab, and 26) displayed curare-like effects of ultrashort duration in rhesus monkeys.
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Affiliation(s)
- I Kaldor
- Division of Medicinal Chemistry, GlaxoSmithKline Research & Development, Five Moore Drive, Research Triangle Park, NC 27709, USA
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25
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Samano V, Ray JA, Thompson JB, Mook RA, Jung DK, Koble CS, Martin MT, Bigham EC, Regitz CS, Feldman PL, Boros EE. Synthesis of ultra-short-acting neuromuscular blocker GW 0430: a remarkably stereo- and regioselective synthesis of mixed tetrahydroisoquinolinium chlorofumarates. Org Lett 1999; 1:1993-6. [PMID: 10836056 DOI: 10.1021/ol9911573] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[formula: see text] The stereo- and regioselective synthesis of ultra-short-acting nondepolarizing neuromuscular blocker GW 0430 (5a) is described. Key steps involved the enantioselective transfer hydrogenation of imine 8 employing Noyori's catalyst, the stereoselective crystallization and methanolysis of trans-bataines 11 and 12, and the stereo- and regioselective trans elimination of hydrogen chloride from 14. The latter transformation allowed complete control of the position of the chloro substituent and stereochemistry at the double bond of the linker in 15.
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Affiliation(s)
- V Samano
- Department of Chemistry, Glaxo Wellcome Research and Development, Research Triangle Park, North Carolina 27709, USA.
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26
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Lawrence CC, Gerfen GJ, Samano V, Nitsche R, Robins MJ, Rétey J, Stubbe J. Binding of Cob(II)alamin to the adenosylcobalamin-dependent ribonucleotide reductase from Lactobacillus leichmannii. Identification of dimethylbenzimidazole as the axial ligand. J Biol Chem 1999; 274:7039-42. [PMID: 10066759 DOI: 10.1074/jbc.274.11.7039] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ribonucleoside triphosphate reductase (RTPR) from Lactobacillus leichmannii catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates and uses coenzyme B12, adenosylcobalamin (AdoCbl), as a cofactor. Use of a mechanism-based inhibitor, 2'-deoxy-2'-methylenecytidine 5'-triphosphate, and isotopically labeled RTPR and AdoCbl in conjunction with EPR spectroscopy has allowed identification of the lower axial ligand of cob(II)alamin when bound to RTPR. In common with the AdoCbl-dependent enzymes catalyzing irreversible heteroatom migrations and in contrast to the enzymes catalyzing reversible carbon skeleton rearrangements, the dimethylbenzimidazole moiety of the cofactor is not displaced by a protein histidine upon binding to RTPR.
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Affiliation(s)
- C C Lawrence
- Departments of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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27
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Boros EE, Bigham EC, Boswell GE, Mook RA, Patel SS, Savarese JJ, Ray JA, Thompson JB, Hashim MA, Wisowaty JC, Feldman PL, Samano V. Bis- and mixed-tetrahydroisoquinolinium chlorofumarates: new ultra-short-acting nondepolarizing neuromuscular blockers. J Med Chem 1999; 42:206-9. [PMID: 9925724 DOI: 10.1021/jm980597h] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- E E Boros
- Glaxo Wellcome Research and Development, Five Moore Drive, Research Triangle Park, North Carolina 27709, USA
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28
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van der Donk WA, Yu G, Pérez L, Sanchez RJ, Stubbe J, Samano V, Robins MJ. Detection of a new substrate-derived radical during inactivation of ribonucleotide reductase from Escherichia coli by gemcitabine 5'-diphosphate. Biochemistry 1998; 37:6419-26. [PMID: 9572859 DOI: 10.1021/bi9729357] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ribonucleotide reductases (RNRs) play a central role in replication and repair by catalyzing the conversion of nucleotides to deoxynucleotides. Gemcitabine 5'-diphosphate (F2CDP), the nucleoside of which was recently approved by the FDA for treatment of pancreatic cancer, is a potent mechanism-based inhibitor of class I and II RNRs. Inactivation of the Eschericia coli class I RNR is accompanied by loss of two fluorides and one cytosine. This RNR is composed of two homodimeric subunits: R1 and R2. R1 is the site of nucleotide reduction, and R2 contains the essential diferric-tyrosyl radical cofactor. The mechanism of inactivation depends on the availability of reductant. In the presence of reductant [thioredoxin (TR)/thioredoxin reductase (TRR)/NADPH or dithiothreitol], inhibition results from R1 inactivation. In the absence of reductant with prereduced R1 and R2, inhibition results from loss of the essential tyrosyl radical in R2. The same result is obtained with C754S/C759S-R1 in the presence of TR/TRR/NADPH. In both cases, tyrosyl radical loss is accompanied by formation of a new stable radical (0.15-0.25 equiv/RNR). EPR studies in 2H2O, with [U-2H]R1, and examination of the microwave power saturation of the observed signal, indicate by process of elimination that this new radical is nucleotide-based. In contrast to all previously investigated 2'-substituted nucleotide inhibitors of RNR, inactivation is not accompanied by formation of a new protein-associated chromophore under any conditions. The requirement for reductant in the R1 inactivation pathway, the lack of chromophore on the protein, the loss of two fluoride ions, and the stoichiometry of the inactivation all suggest a unique mechanism of RNR inactivation not previously observed with other 2'-substituted nucleotide inhibitors of RNR. This unique mode of inactivation is proposed to be responsible for its observed clinical efficacy.
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Affiliation(s)
- W A van der Donk
- Chemistry Department, Brigham Young University, 225 Eyring Science Center, P.O. Box 24672, Provo, Utah 84602-4672, USA
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29
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Silva DJ, Stubbe J, Samano V, Robins MJ. Gemcitabine 5'-triphosphate is a stoichiometric mechanism-based inhibitor of Lactobacillus leichmannii ribonucleoside triphosphate reductase: evidence for thiyl radical-mediated nucleotide radical formation. Biochemistry 1998; 37:5528-35. [PMID: 9548936 DOI: 10.1021/bi972934e] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ribonucleoside triphosphate reductase (RTPR) from Lactobacillus leichmannii utilizes adenosylcobalamin and catalyzes the conversion of nucleoside triphosphates to deoxynucleoside triphosphates. One equivalent of 2',2'-difluoro-2'-deoxycytidine 5'-triphosphate, F2dCTP, rapidly inactivates RTPR. Analysis of the reaction products reveals that inactivation is accompanied by release of two fluoride ions and 0.84 equiv of 5'-deoxyadenosine and attachment of 1 equiv of corrin covalently to an active-site cysteine residue of RTPR. No cytosine release was detected. Proteolysis of corrin-labeled RTPR with endoproteinase Glu-C and peptide mapping at pH 5.8 revealed that C419 was predominantly modified. The kinetics of the inactivation have been examined by stopped-flow (SF) UV-vis spectroscopy and rapid freeze quench (RFQ) electron paramagnetic resonance (EPR) spectroscopy. Monitoring DeltaA525 nm shows that cob(II)alamin is formed with an apparent kobs of 50 s-1, only 2. 5-fold slower than a similar experiment carried out with cytidine 5'-triphosphate (CTP). The same reaction mixture was thus quenched at times from 22 ms to 30 s and examined by EPR spectroscopy. At early time points the EPR spectrum resembled a thiyl radical exchange coupled to cob(II)alamin. From 22 to 255 ms the total spin concentration remained unchanged at 1.4 spins/RTPR, twice that predicted by the amount of cob(II)alamin determined by SF. However, with time the signal attributed to the thiyl radical-cob(II)alamin disappears and new signal(s) with broad feature(s) at g = 2.33 and a sharp feature at g = 2.00 appeared, suggesting formation of cob(II)alamin and a nucleotide-based radical with only dipolar interactions. These studies have been interpreted to support the proposal that an RTPR-based thiyl radical can give rise to a nucleotide-based radical.
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Affiliation(s)
- D J Silva
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
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30
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Robins MJ, Sarker S, Samano V, Wnuk SF. Nucleic Acid Related Compounds. 94. Remarkably High Stereoselective Reductions of 2′- and 3′-Ketonucleoside Derivatives To Give Arabino, Ribo, and Xylofuranosyl Nucleosides with Hydrogen Isotopes at C2′ and C3′. Tetrahedron 1997. [DOI: 10.1016/s0040-4020(96)01035-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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31
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Robins M, Samano M, Samano V. Ribonucleotide Reductase Targets for Chemotherapy; Mechanistic Aspects and Biologically Active Agents. Nucleosides, Nucleotides & Nucleic Acids 1995. [DOI: 10.1080/15257779508012411] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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32
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Samano V, Robins MJ. Synthesis of 3′-deoxyadenosine-3′-spirocyclopropane, 3′-deoxy-uridine-3′-spirocyclopropane, and 5′-deoxy-4′,5′-methanoadenosine. Tetrahedron Lett 1994. [DOI: 10.1016/s0040-4039(00)73206-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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33
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Cory AH, Samano V, Robins MJ, Cory JG. 2'-Deoxy-2'-methylene derivatives of adenosine, guanosine, tubercidin, cytidine and uridine as inhibitors of L1210 cell growth in culture. Biochem Pharmacol 1994; 47:365-71. [PMID: 8304981 DOI: 10.1016/0006-2952(94)90028-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The 2'-deoxy-2'-methylene derivatives of adenosine (MdAdo), guanosine (MdGuo), tubercidin (MdTu), cytidine (MdCyd) and uridine (MdUrd) were synthesized as mechanism-based inhibitors directed at ribonucleotide reductase. It was shown that MdCyd 5'-diphosphate irreversibly inactivated ribonucleotide reductase from Escherichia coli (Baker et al., J Med Chem 34: 1879-1884, 1991). In studies reported here, MdAdo/EHNA, MdGuo and MdCyd inhibited L1210 cell growth with IC50 values of 3.4, 10.6 and 1.4 microM, respectively. Since MdAdo is a substrate for adenosine deaminase, the presence of EHNA was required to give maximal growth inhibition. 8-Aminoguanosine was not required to maximize the cytotoxic effects of MdGuo. The 2'-deoxy-2'-methylene derivatives of tubercidin and uridine did not inhibit L1210 cell growth at concentrations as high as 50 microM (MdTu) or 100 microM (MdUrd). L1210 cell lines resistant to hydroxyurea (directed at the non-heme iron subunit of ribonucleotide reductase) or deoxyadenosine (directed at the effector binding subunit of ribonucleotide reductase) were not resistant to MdCyd. An L1210 cell line that was highly resistant to dGuo due to the loss of a relatively specific deoxyribonucleoside kinase (Cory et al., J Biol Chem 268: 405-409, 1993) had a 6.6-fold increase in the IC50 value toward MdCyd, but showed only a 2-fold increase in resistance to MdGuo. Another L1210 cell line that was markedly deficient in adenosine kinase activity was highly resistant to MdAdo. Analysis by flow cytometry showed that MdCyd showed the transit of the cells through the G2/M phase of the cell cycle resulting in the buildup of the G2/M population. MdAdo, MdGuo and MdCyd inhibited the incorporation of [14C]cytidine into DNA without an effect on RNA synthesis or total cellular uptake of [14C]cytidine. The conversion of [14C]cytidine to deoxycytidine nucleotides was partially inhibited by MdGuo, but not by MdAdo or MdCyd. These data show that the 2'-deoxy-2'-methylene derivatives of adenosine, guanosine and cytidine are activated via specific nucleoside kinases and that the modes of action of these compounds are not identical.
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Affiliation(s)
- A H Cory
- Department of Biochemistry, East Carolina University, School of Medicine, Greenville 27858
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Robins MJ, Samano V, Zhang W, Balzarini J, De Clercq E, Borchardt RT, Lee Y, Yuan CS. Nucleic acid related compounds. 74. Synthesis and biological activity of 2'(and 3')-deoxy-2'(and 3')-methylenenucleoside analogues that function as mechanism-based inhibitors of S-adenosyl-L-homocysteine hydrolase and/or ribonucleotide reductase. J Med Chem 1992; 35:2283-93. [PMID: 1613752 DOI: 10.1021/jm00090a020] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Treatment of 2-amino-6-chloro-9-(beta-D-ribofuranosyl)purine (21) with TBDMS chloride/imidazole/DMF gave a separable mixture of 5'-O, 2',5'-bis-O (22), 3',5'-bis-O (23), and 2',3',5'-tris-O-TBDMS derivatives. Oxidation of 22 and 23 with CrO3/pyridine/Ac2O, treatment of the respective ketonucleosides with methylenetriphenylphosphorane, and deprotection gave 2-amino-6-chloro-9-[3(and 2)-deoxy-3(and 2)-methylene- beta-D-erythro-pentofuranosyl]purines (28 and 37) that were converted into other 2-amino-6-substituted-purine analogues. Tubercidin was converted into 2'-deoxy-2'-methylenetubercidin (49) by an analogous route. Inactivation of S-adenosyl-L-homocysteine hydrolase by 2'- and 3'-methyleneadenosine analogues was investigated. Mechanism-based inhibition of S-adenosyl-L-homocysteine hydrolase and anticancer and antiviral activities of 2'(and 3')-deoxy-2'(and 3')-methylenenucleoside analogues are discussed.
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Affiliation(s)
- M J Robins
- Department of Chemistry, Brigham Young University, Provo, Utah 84602
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Baker CH, Banzon J, Bollinger JM, Stubbe J, Samano V, Robins MJ, Lippert B, Jarvi E, Resvick R. 2'-Deoxy-2'-methylenecytidine and 2'-deoxy-2',2'-difluorocytidine 5'-diphosphates: potent mechanism-based inhibitors of ribonucleotide reductase. J Med Chem 1991; 34:1879-84. [PMID: 2061926 DOI: 10.1021/jm00110a019] [Citation(s) in RCA: 186] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
It has been found that 2'-deoxy-2'-methyleneuridine (MdUrd), 2'-deoxy-2'-methylenecytidine (MdCyd), and 2'-deoxy-2',2'-difluorocytidine (dFdCyd) 5'-diphosphates (MdUDP (1) MdCDP (2) and dFdCDP (3), respectively) function as irreversible inactivators of the Escherichia coli ribonucleoside diphosphate reductase (RDPR). 2 is a much more potent inhibitor than its uridine analogue 1. It is proposed that 2 undergoes abstraction of H3' to give an allylic radical that captures a hydrogen atom and decomposes to an active alkylating furanone species. RDPR also accepts 3 as an alternative substrate analogue and presumably executes an initial abstraction of H3' to initiate formation of a suicide species. Both 2 and 3 give inactivation results that differ from those of previously studied inhibitors. The potent anticancer activities of MdCyd and dFdCyd indicate a significant chemotherapeutic potential. The analogous RDPR of mammalian cells should be regarded as a likely target and/or activating enzyme for these novel mechanism-based inactivators.
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Affiliation(s)
- C H Baker
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139
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Samano V, Robins MJ. Stereoselective Addition of a Wittig Reagent To Give a Single Nucleoside Oxaphosphetane Diastereoisomer. Synthesis of 2′(and 3′)-Deoxy-2′(and 3′)-methyleneuridine (and cytidine) Derivatives from Uridine Ketonucleosides. SYNTHESIS-STUTTGART 1991. [DOI: 10.1055/s-1991-26774] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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