1
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Hembre E, Early JV, Odingo J, Shelton C, Anoshchenko O, Guzman J, Flint L, Dennison D, McNeil MB, Korkegian A, Ovechkina Y, Ornstein P, Masquelin T, Hipskind PA, Parish T. Novel Trifluoromethyl Pyrimidinone Compounds With Activity Against Mycobacterium tuberculosis. Front Chem 2021; 9:613349. [PMID: 33996738 PMCID: PMC8117417 DOI: 10.3389/fchem.2021.613349] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 03/05/2021] [Indexed: 11/13/2022] Open
Abstract
The identification and development of new anti-tubercular agents are a priority research area. We identified the trifluoromethyl pyrimidinone series of compounds in a whole-cell screen against Mycobacterium tuberculosis. Fifteen primary hits had minimum inhibitory concentrations (MICs) with good potency IC90 is the concentration at which M. tuberculosis growth is inhibited by 90% (IC90 < 5 μM). We conducted a structure-activity relationship investigation for this series. We designed and synthesized an additional 44 molecules and tested all analogs for activity against M. tuberculosis and cytotoxicity against the HepG2 cell line. Substitution at the 5-position of the pyrimidinone with a wide range of groups, including branched and straight chain alkyl and benzyl groups, resulted in active molecules. Trifluoromethyl was the preferred group at the 6-position, but phenyl and benzyl groups were tolerated. The 2-pyridyl group was required for activity; substitution on the 5-position of the pyridyl ring was tolerated but not on the 6-position. Active molecules from the series demonstrated low selectivity, with cytotoxicity against eukaryotic cells being an issue. However, there were active and non-cytotoxic molecules; the most promising molecule had an MIC (IC90) of 4.9 μM with no cytotoxicity (IC50 > 100 μM). The series was inactive against Gram-negative bacteria but showed good activity against Gram-positive bacteria and yeast. A representative molecule from this series showed rapid concentration-dependent bactericidal activity against replicating M. tuberculosis bacilli with ~4 log kill in <7 days. Overall the biological properties were promising, if cytotoxicity could be reduced. There is scope for further medicinal chemistry optimization to improve the properties without major change in structural features.
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Affiliation(s)
- Erik Hembre
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
| | - Julie V Early
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Joshua Odingo
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Catherine Shelton
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Olena Anoshchenko
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Junitta Guzman
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Lindsay Flint
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Devon Dennison
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Matthew B McNeil
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Aaron Korkegian
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Yulia Ovechkina
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Paul Ornstein
- Apollo Drug Discovery Consulting, LLC, Northbrook, IL, United States
| | - Thierry Masquelin
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
| | - Philip A Hipskind
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
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2
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Ray P, Huggett M, Turner PA, Taylor M, Cleghorn LAT, Early J, Kumar A, Bonnett SA, Flint L, Joerss D, Johnson J, Korkegian A, Mullen S, Moure AL, Davis SH, Murugesan D, Mathieson M, Caldwell N, Engelhart CA, Schnappinger D, Epemolu O, Zuccotto F, Riley J, Scullion P, Stojanovski L, Massoudi L, Robertson GT, Lenaerts AJ, Freiberg G, Kempf DJ, Masquelin T, Hipskind PA, Odingo J, Read KD, Green SR, Wyatt PG, Parish T. Spirocycle MmpL3 Inhibitors with Improved hERG and Cytotoxicity Profiles as Inhibitors of Mycobacterium tuberculosis Growth. ACS Omega 2021; 6:2284-2311. [PMID: 33521468 PMCID: PMC7841955 DOI: 10.1021/acsomega.0c05589] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/21/2020] [Indexed: 05/10/2023]
Abstract
With the emergence of multi-drug-resistant strains of Mycobacterium tuberculosis, there is a pressing need for new oral drugs with novel mechanisms of action. A number of scaffolds with potent anti-tubercular in vitro activity have been identified from phenotypic screening that appear to target MmpL3. However, the scaffolds are typically lipophilic, which facilitates partitioning into hydrophobic membranes, and several contain basic amine groups. Highly lipophilic basic amines are typically cytotoxic against mammalian cell lines and have associated off-target risks, such as inhibition of human ether-à-go-go related gene (hERG) and IKr potassium current modulation. The spirocycle compound 3 was reported to target MmpL3 and displayed promising efficacy in a murine model of acute tuberculosis (TB) infection. However, this highly lipophilic monobasic amine was cytotoxic and inhibited the hERG ion channel. Herein, the related spirocycles (1-2) are described, which were identified following phenotypic screening of the Eli Lilly corporate library against M. tuberculosis. The novel N-alkylated pyrazole portion offered improved physicochemical properties, and optimization led to identification of a zwitterion series, exemplified by lead 29, with decreased HepG2 cytotoxicity as well as limited hERG ion channel inhibition. Strains with mutations in MmpL3 were resistant to 29, and under replicating conditions, 29 demonstrated bactericidal activity against M. tuberculosis. Unfortunately, compound 29 had no efficacy in an acute model of TB infection; this was most likely due to the in vivo exposure remaining above the minimal inhibitory concentration for only a limited time.
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Affiliation(s)
- Peter
C. Ray
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Margaret Huggett
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Penelope A. Turner
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Malcolm Taylor
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Laura A. T. Cleghorn
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Julie Early
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Anuradha Kumar
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Shilah A. Bonnett
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Lindsay Flint
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Douglas Joerss
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - James Johnson
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Aaron Korkegian
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Steven Mullen
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Abraham L. Moure
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Susan H. Davis
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Dinakaran Murugesan
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Michael Mathieson
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Nicola Caldwell
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Curtis A. Engelhart
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Dirk Schnappinger
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Ola Epemolu
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Fabio Zuccotto
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Jennifer Riley
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Paul Scullion
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Laste Stojanovski
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Lisa Massoudi
- Mycobacteria
Research Laboratories, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Gregory T. Robertson
- Mycobacteria
Research Laboratories, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Anne J. Lenaerts
- Mycobacteria
Research Laboratories, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Gail Freiberg
- AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Dale J. Kempf
- AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Thierry Masquelin
- Discovery
Chemistry Research, Eli Lilly and Company, Lilly Corporate Centre, MC/87/02/203, G17, Indianapolis, Indiana 46285, United States
| | | | - Joshua Odingo
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Kevin D. Read
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Simon R. Green
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Paul G. Wyatt
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Tanya Parish
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
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3
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Affiliation(s)
- Christos A. Nicolaou
- Discovery Chemistry, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Ian A. Watson
- Discovery Chemistry, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Mark LeMasters
- Research Chemistry IT, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Thierry Masquelin
- Discovery Chemistry, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Jibo Wang
- Discovery Chemistry, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
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4
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Early J, Ollinger J, Darby C, Alling T, Mullen S, Casey A, Gold B, Ochoada J, Wiernicki T, Masquelin T, Nathan C, Hipskind PA, Parish T. Identification of Compounds with pH-Dependent Bactericidal Activity against Mycobacterium tuberculosis. ACS Infect Dis 2019; 5:272-280. [PMID: 30501173 PMCID: PMC6371205 DOI: 10.1021/acsinfecdis.8b00256] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
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To find new inhibitors of Mycobacterium tuberculosis that have novel mechanisms of
action, we miniaturized a high throughput
screen to identify compounds that disrupt pH homeostasis. We adapted
and validated a 384-well format assay to determine intrabacterial
pH using a ratiometric green fluorescent protein. We screened 89000
small molecules under nonreplicating conditions and confirmed 556
hits that reduced intrabacterial pH (below pH 6.5). We selected five
compounds that disrupt intrabacterial pH homeostasis and also showed
some activity against nonreplicating bacteria in a 4-stress model,
but with no (or greatly reduced) activity against replicating bacteria.
The compounds selected were two benzamide sulfonamides, a benzothiadiazole,
a bissulfone, and a thiadiazole, none of which are known antibacterial
agents. All of these five compounds demonstrated bactericidal activity
against nonreplicating bacteria in buffer. Four of the five compounds
demonstrated increased activity under low pH conditions. None of the
five compounds acted as ionophores or as general disrupters of membrane
potential. These compounds are useful starting points for work to
elucidate their mechanism of action and their utility for drug discovery.
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Affiliation(s)
- Julie Early
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue E, Suite 400, Seattle, Washington 98102, United States
| | - Juliane Ollinger
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue E, Suite 400, Seattle, Washington 98102, United States
| | - Crystal Darby
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, Box 62, New York, New York 10065, United States
| | - Torey Alling
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue E, Suite 400, Seattle, Washington 98102, United States
| | - Steven Mullen
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue E, Suite 400, Seattle, Washington 98102, United States
| | - Allen Casey
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue E, Suite 400, Seattle, Washington 98102, United States
| | - Ben Gold
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, Box 62, New York, New York 10065, United States
| | - Jason Ochoada
- Lilly Research Laboratories, Eli Lilly and Company, 307 E Merrill Street, Indianapolis, Indiana 46285, United States
| | - Todd Wiernicki
- Lilly Research Laboratories, Eli Lilly and Company, 307 E Merrill Street, Indianapolis, Indiana 46285, United States
| | - Thierry Masquelin
- Lilly Research Laboratories, Eli Lilly and Company, 307 E Merrill Street, Indianapolis, Indiana 46285, United States
| | - Carl Nathan
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, Box 62, New York, New York 10065, United States
| | - Philip A. Hipskind
- Lilly Research Laboratories, Eli Lilly and Company, 307 E Merrill Street, Indianapolis, Indiana 46285, United States
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue E, Suite 400, Seattle, Washington 98102, United States
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5
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Cleghorn LAT, Ray PC, Odingo J, Kumar A, Wescott H, Korkegian A, Masquelin T, Lopez Moure A, Wilson C, Davis S, Huggett M, Turner P, Smith A, Epemolu O, Zuccotto F, Riley J, Scullion P, Shishikura Y, Ferguson L, Rullas J, Guijarro L, Read KD, Green SR, Hipskind P, Parish T, Wyatt PG. Identification of Morpholino Thiophenes as Novel Mycobacterium tuberculosis Inhibitors, Targeting QcrB. J Med Chem 2018; 61:6592-6608. [PMID: 29944372 PMCID: PMC6089501 DOI: 10.1021/acs.jmedchem.8b00172] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [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: 01/02/2023]
Abstract
With the emergence of multidrug-resistant strains of Mycobacterium tuberculosis there is a pressing need for new oral drugs with novel mechanisms of action. Herein, we describe the identification of a novel morpholino-thiophenes (MOT) series following phenotypic screening of the Eli Lilly corporate library against M. tuberculosis strain H37Rv. The design, synthesis, and structure-activity relationships of a range of analogues around the confirmed actives are described. Optimized leads with potent whole cell activity against H37Rv, no cytotoxicity flags, and in vivo efficacy in an acute murine model of infection are described. Mode-of-action studies suggest that the novel scaffold targets QcrB, a subunit of the menaquinol cytochrome c oxidoreductase, part of the bc1-aa3-type cytochrome c oxidase complex that is responsible for driving oxygen-dependent respiration.
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Affiliation(s)
- Laura A T Cleghorn
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
| | - Peter C Ray
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
| | - Joshua Odingo
- TB Discovery Research , Infectious Disease Research Institute (IDRI) , 1616 Eastlake Avenue East, Suite 400 , Seattle , Washington 98102 , United States
| | - Anuradha Kumar
- TB Discovery Research , Infectious Disease Research Institute (IDRI) , 1616 Eastlake Avenue East, Suite 400 , Seattle , Washington 98102 , United States
| | - Heather Wescott
- TB Discovery Research , Infectious Disease Research Institute (IDRI) , 1616 Eastlake Avenue East, Suite 400 , Seattle , Washington 98102 , United States
| | - Aaron Korkegian
- TB Discovery Research , Infectious Disease Research Institute (IDRI) , 1616 Eastlake Avenue East, Suite 400 , Seattle , Washington 98102 , United States
| | - Thierry Masquelin
- Eli Lilly and Company, Discovery Chemistry Research, Lilly Corporate Centre , MC/87/02/203, G17, Indianapolis , Indiana 46285 , United States
| | - Abraham Lopez Moure
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
| | - Caroline Wilson
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
| | - Susan Davis
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
| | - Margaret Huggett
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
| | - Penelope Turner
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
| | - Alasdair Smith
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
| | - Ola Epemolu
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
| | - Fabio Zuccotto
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
| | - Jennifer Riley
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
| | - Paul Scullion
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
| | - Yoko Shishikura
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
| | - Liam Ferguson
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
| | - Joaquin Rullas
- Diseases of the Developing World , GlaxoSmithKline , Calle Severo Ochoa 2 , 28760 Tres Cantos , Madrid Spain
| | - Laura Guijarro
- Diseases of the Developing World , GlaxoSmithKline , Calle Severo Ochoa 2 , 28760 Tres Cantos , Madrid Spain
| | - Kevin D Read
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
| | - Simon R Green
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
| | - Phil Hipskind
- Eli Lilly and Company, Discovery Chemistry Research, Lilly Corporate Centre , MC/87/02/203, G17, Indianapolis , Indiana 46285 , United States
| | - Tanya Parish
- TB Discovery Research , Infectious Disease Research Institute (IDRI) , 1616 Eastlake Avenue East, Suite 400 , Seattle , Washington 98102 , United States
| | - Paul G Wyatt
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences , University of Dundee , Dundee DD1 5EH , United Kingdom
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6
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Chandrasekera NS, Berube BJ, Shetye G, Chettiar S, O’Malley T, Manning A, Flint L, Awasthi D, Ioerger TR, Sacchettini J, Masquelin T, Hipskind PA, Odingo J, Parish T. Improved Phenoxyalkylbenzimidazoles with Activity against Mycobacterium tuberculosis Appear to Target QcrB. ACS Infect Dis 2017; 3:898-916. [PMID: 29035551 PMCID: PMC5727484 DOI: 10.1021/acsinfecdis.7b00112] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
The phenoxy alkyl benzimidazoles
(PABs) have good antitubercular activity. We expanded our structure–activity
relationship studies to determine the core components of PABs required
for activity. The most potent compounds had minimum inhibitory concentrations
against Mycobacterium tuberculosis in the low nanomolar
range with very little cytotoxicity against eukaryotic cells as well
as activity against intracellular bacteria. We isolated resistant
mutants against PAB compounds, which had mutations in either Rv1339,
of unknown function, or qcrB, a component of the
cytochrome bc1 oxidase of the electron
transport chain. QcrB mutant strains were resistant to all PAB compounds,
whereas Rv1339 mutant strains were only resistant to a subset, suggesting
that QcrB is the target. The discovery of the target for PAB compounds
will allow for the improved design of novel compounds to target intracellular M. tuberculosis.
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Affiliation(s)
- N. Susantha Chandrasekera
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Bryan J. Berube
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Gauri Shetye
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Somsundaram Chettiar
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Theresa O’Malley
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Alyssa Manning
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Lindsay Flint
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Divya Awasthi
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | | | | | - Thierry Masquelin
- Lilly Research Laboratories, 307 East Merrill Street, Indianapolis, Indiana 46285, United States
| | - Philip A. Hipskind
- Lilly Research Laboratories, 307 East Merrill Street, Indianapolis, Indiana 46285, United States
| | - Joshua Odingo
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
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7
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Odingo J, Bailey MA, Files M, Early JV, Alling T, Dennison D, Bowman J, Dalai S, Kumar N, Cramer J, Masquelin T, Hipskind PA, Parish T. In Vitro Evaluation of Novel Nitazoxanide Derivatives against Mycobacterium tuberculosis. ACS Omega 2017; 2:5873-5890. [PMID: 30023755 PMCID: PMC6044914 DOI: 10.1021/acsomega.7b00892] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 08/17/2017] [Indexed: 06/08/2023]
Abstract
Nitazoxanide has antiparasitic and antibiotic activities including activity against Mycobacterium tuberculosis. We prepared and evaluated a set of its analogues to determine the structure-activity relationship, and identified several amide- and urea-based analogues with low micromolar activity against M. tuberculosis in vitro. Pharmacokinetics in the rat suggested a path forward to obtain bioavailable compounds. The series had a good microbiological profile with bactericidal activity in vitro against replicating and nonreplicating M. tuberculosis. Analogues had limited activity against other Gram-positive bacteria but no activity against Gram-negative bacteria. Our studies identified the key liability in this series as cytotoxicity. Future work concentrating on identifying the target(s) could assist in removing activity against eukaryotic cells.
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Affiliation(s)
- Joshua Odingo
- Infectious
Disease Research Institute, TB Discovery Research, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Mai A. Bailey
- Infectious
Disease Research Institute, TB Discovery Research, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Megan Files
- Infectious
Disease Research Institute, TB Discovery Research, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Julie V. Early
- Infectious
Disease Research Institute, TB Discovery Research, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Torey Alling
- Infectious
Disease Research Institute, TB Discovery Research, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Devon Dennison
- Infectious
Disease Research Institute, TB Discovery Research, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | - Julie Bowman
- Infectious
Disease Research Institute, TB Discovery Research, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
| | | | - Naresh Kumar
- Jubilant
Chemsys Limited, B-34,
Sector 58, 201301 Noida, India
| | - Jeffrey Cramer
- Eli
Lilly and Company, Lilly Research Laboratories, Indianapolis, Indiana 46285, United States
| | - Thierry Masquelin
- Eli
Lilly and Company, Lilly Research Laboratories, Indianapolis, Indiana 46285, United States
| | - Philip A. Hipskind
- Eli
Lilly and Company, Lilly Research Laboratories, Indianapolis, Indiana 46285, United States
| | - Tanya Parish
- Infectious
Disease Research Institute, TB Discovery Research, 1616 Eastlake Avenue East, Seattle, Washington 98102, United States
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8
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Zuniga ES, Korkegian A, Mullen S, Hembre EJ, Ornstein PL, Cortez G, Biswas K, Kumar N, Cramer J, Masquelin T, Hipskind PA, Odingo J, Parish T. The synthesis and evaluation of triazolopyrimidines as anti-tubercular agents. Bioorg Med Chem 2017; 25:3922-3946. [PMID: 28576632 PMCID: PMC5513444 DOI: 10.1016/j.bmc.2017.05.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/10/2017] [Accepted: 05/15/2017] [Indexed: 11/12/2022]
Abstract
We identified a di-substituted triazolopyrimidine with anti-tubercular activity against Mycobacterium tuberculosis. Three segments of the scaffold were examined rationally to establish a structure-activity relationship with the goal of improving potency and maintaining good physicochemical properties. A number of compounds displayed sub-micromolar activity against Mycobacterium tuberculosis with no cytotoxicity against eukaryotic cells. Non-substituted aromatic rings at C5 and a two-carbon chain connecting a terminal aromatic at C7 were preferred features; the presence of NH at C7 and a lack of substituent at C2 were essential for potency. We identified compounds with acceptable metabolic stability in rodent and human liver microsomes. Our findings suggest that the easily-synthesized triazolopyrimidines are a promising class of potent anti-tubercular agents and warrant further investigation in our search for new drugs to fight tuberculosis.
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Affiliation(s)
- Edison S Zuniga
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, WA 98102, USA
| | - Aaron Korkegian
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, WA 98102, USA
| | - Steven Mullen
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, WA 98102, USA
| | - Erik J Hembre
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Paul L Ornstein
- Roosevelt University College of Pharmacy, Schaumburg, IL 60173, USA
| | - Guillermo Cortez
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | | | - Naresh Kumar
- Jubilant Chemsys Limited, B-34, Sector 58, Noida 201301, India
| | - Jeffrey Cramer
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Thierry Masquelin
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Philip A Hipskind
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Joshua Odingo
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, WA 98102, USA
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Seattle, WA 98102, USA.
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9
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Sarathy JP, Zuccotto F, Hsinpin H, Sandberg L, Via LE, Marriner GA, Masquelin T, Wyatt P, Ray P, Dartois V. Prediction of Drug Penetration in Tuberculosis Lesions. ACS Infect Dis 2016; 2:552-63. [PMID: 27626295 DOI: 10.1021/acsinfecdis.6b00051] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The penetration of antibiotics in necrotic tuberculosis lesions is heterogeneous and drug-specific, but the factors underlying such differential partitioning are unknown. We hypothesized that drug binding to macromolecules in necrotic foci (or caseum) prevents passive drug diffusion through avascular caseum, a critical site of infection. Using a caseum binding assay and MALDI mass spectrometry imaging of tuberculosis drugs, we showed that binding to caseum inversely correlates with passive diffusion into the necrotic core. We developed a high-throughput assay relying on rapid equilibrium dialysis and a caseum surrogate designed to mimic the composition of native caseum. A set of 279 compounds was profiled in this assay to generate a large data set and explore the physicochemical drivers of free diffusion into caseum. Principle component analysis and modeling of the data set delivered an in silico signature predictive of caseum binding, combining 69 molecular descriptors. Among the major positive drivers of binding were high lipophilicity and poor solubility. Determinants of molecular shape such as the number of rings, particularly aromatic rings, number of sp(2) carbon counts, and volume-to-surface ratio negatively correlated with the free fraction, indicating that low-molecular-weight nonflat compounds are more likely to exhibit low caseum binding properties and diffuse effectively through caseum. To provide simple guidance in the property-based design of new compounds, a rule of thumb was derived whereby the sum of the hydrophobicity (clogP) and aromatic ring count is proportional to caseum binding. These tools can be used to ensure desirable lesion partitioning and guide the selection of optimal regimens against tuberculosis.
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Affiliation(s)
- Jansy P. Sarathy
- Public Health Research
Institute Centre, New Jersey Medical School, Rutgers, 225 Warren Street, Newark, New Jersey 07103, United States
| | - Fabio Zuccotto
- Drug Discovery Unit,
Division of Biological Chemistry and Drug Discovery, Sir James Black
Centre, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Ho Hsinpin
- Public Health Research
Institute Centre, New Jersey Medical School, Rutgers, 225 Warren Street, Newark, New Jersey 07103, United States
| | - Lars Sandberg
- Drug Discovery Unit,
Division of Biological Chemistry and Drug Discovery, Sir James Black
Centre, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Laura E. Via
- Tuberculosis
Research Section, Laboratory of Clinical Infectious Diseases, NIAID, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Gwendolyn A. Marriner
- Tuberculosis
Research Section, Laboratory of Clinical Infectious Diseases, NIAID, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Thierry Masquelin
- Discovery Chemistry Research, Lilly Corporate Center,
Eli Lilly and Company, 893 S. Delaware, MC/87/02/203 G17, Indianapolis, Indiana 46285, United States
| | - Paul Wyatt
- Drug Discovery Unit,
Division of Biological Chemistry and Drug Discovery, Sir James Black
Centre, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Peter Ray
- Drug Discovery Unit,
Division of Biological Chemistry and Drug Discovery, Sir James Black
Centre, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Véronique Dartois
- Public Health Research
Institute Centre, New Jersey Medical School, Rutgers, 225 Warren Street, Newark, New Jersey 07103, United States
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10
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Kesicki EA, Bailey MA, Ovechkina Y, Early JV, Alling T, Bowman J, Zuniga ES, Dalai S, Kumar N, Masquelin T, Hipskind PA, Odingo JO, Parish T. Synthesis and Evaluation of the 2-Aminothiazoles as Anti-Tubercular Agents. PLoS One 2016; 11:e0155209. [PMID: 27171280 PMCID: PMC4865136 DOI: 10.1371/journal.pone.0155209] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 04/26/2016] [Indexed: 11/19/2022] Open
Abstract
The 2-aminothiazole series has anti-bacterial activity against the important global pathogen Mycobacterium tuberculosis. We explored the nature of the activity by designing and synthesizing a large number of analogs and testing these for activity against M. tuberculosis, as well as eukaryotic cells. We determined that the C-2 position of the thiazole can accommodate a range of lipophilic substitutions, while both the C-4 position and the thiazole core are sensitive to change. The series has good activity against M. tuberculosis growth with sub-micromolar minimum inhibitory concentrations being achieved. A representative analog was selective for mycobacterial species over other bacteria and was rapidly bactericidal against replicating M. tuberculosis. The mode of action does not appear to involve iron chelation. We conclude that this series has potential for further development as novel anti-tubercular agents.
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Affiliation(s)
- Edward A. Kesicki
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - Mai A. Bailey
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - Yulia Ovechkina
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - Julie V. Early
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - Torey Alling
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - Julie Bowman
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - Edison S. Zuniga
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington, United States of America
| | | | - Naresh Kumar
- Jubilant Chemsys Limited, B-34, Sector 58, Noida, India
| | - Thierry Masquelin
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - Philip A. Hipskind
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - Joshua O. Odingo
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington, United States of America
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11
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Chandrasekera NS, Alling T, Bailey MA, Files M, Early JV, Ollinger J, Ovechkina Y, Masquelin T, Desai PV, Cramer JW, Hipskind PA, Odingo JO, Parish T. Identification of Phenoxyalkylbenzimidazoles with Antitubercular Activity. J Med Chem 2015; 58:7273-85. [DOI: 10.1021/acs.jmedchem.5b00546] [Citation(s) in RCA: 34] [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: 01/04/2023]
Affiliation(s)
- N. Susantha Chandrasekera
- Infectious Disease
Research Institute, 1616 Eastlake Avenue
East, Seattle, Washington 98102, United States
| | - Torey Alling
- Infectious Disease
Research Institute, 1616 Eastlake Avenue
East, Seattle, Washington 98102, United States
| | - Mai A. Bailey
- Infectious Disease
Research Institute, 1616 Eastlake Avenue
East, Seattle, Washington 98102, United States
| | - Megan Files
- Infectious Disease
Research Institute, 1616 Eastlake Avenue
East, Seattle, Washington 98102, United States
| | - Julie V. Early
- Infectious Disease
Research Institute, 1616 Eastlake Avenue
East, Seattle, Washington 98102, United States
| | - Juliane Ollinger
- Infectious Disease
Research Institute, 1616 Eastlake Avenue
East, Seattle, Washington 98102, United States
| | - Yulia Ovechkina
- Infectious Disease
Research Institute, 1616 Eastlake Avenue
East, Seattle, Washington 98102, United States
| | - Thierry Masquelin
- Lilly Research
Laboratories, Indianapolis, Indiana 46285, United States
| | - Prashant V. Desai
- Lilly Research
Laboratories, Indianapolis, Indiana 46285, United States
| | - Jeffrey W. Cramer
- Lilly Research
Laboratories, Indianapolis, Indiana 46285, United States
| | | | - Joshua O. Odingo
- Infectious Disease
Research Institute, 1616 Eastlake Avenue
East, Seattle, Washington 98102, United States
| | - Tanya Parish
- Infectious Disease
Research Institute, 1616 Eastlake Avenue
East, Seattle, Washington 98102, United States
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12
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Chavali B, Masquelin T, Nilges MJ, Timm DE, Stout SL, Matter WF, Jin N, Jadhav PK, Deng GG. ESR and X-ray Structure Investigations on the Binding and Mechanism of Inhibition of the Native State of Myeloperoxidase with Low Molecular Weight Fragments. Appl Magn Reson 2015; 46:853-873. [PMID: 26224994 PMCID: PMC4515242 DOI: 10.1007/s00723-015-0698-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 04/01/2015] [Indexed: 03/24/2024]
Abstract
As an early visitor to the injured loci, neutrophil-derived human Myeloperoxidase (hMPO) offers an attractive protein target to modulate the inflammation of the host tissue through suitable inhibitors. We describe a novel methodology of using low temperature ESR spectroscopy (6 K) and FAST™ technology to screen a diverse series of small molecules that inhibit the peroxidase function through reversible binding to the native state of MPO. Our initial efforts to profile molecules on the inhibition of MPO-initiated nitration of the Apo-A1 peptide (AEYHAKATEHL) assay showed several potent (with sub-micro molar IC50s) but spurious inhibitors that either do not bind to the heme pocket in the enzyme or retain high (>50 %) anti oxidant potential. Such molecules when taken forward for X-ray did not yield inhibitor-bound co-crystals. We then used ESR to confirm direct binding to the native state enzyme, by measuring the binding-induced shift in the electronic parameter g to rank order the molecules. Molecules with a higher rank order-those with g-shift Rrelative ≥15-yielded well-formed protein-bound crystals (n = 33 structures). The co-crystal structure with the LSN217331 inhibitor reveals that the chlorophenyl group projects away from the heme along the edges of the Phe366 and Phe407 side chain phenyl rings thereby sterically restricting the access to the heme by the substrates like H2O2. Both ESR and antioxidant screens were used to derive the mechanism of action (reversibility, competitive substrate inhibition, and percent antioxidant potential). In conclusion, our results point to a viable path forward to target the native state of MPO to tame local inflammation.
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Affiliation(s)
- Balagopalakrishna Chavali
- />Division of Tailored Therapeutics and Imaging, Lilly Corporate Center, Eli Lilly and Company, Bldg.87/C04, Column S17 DC 1940, 893 S Delaware Street, Indianapolis, IN 46285 USA
| | - Thierry Masquelin
- />Discovery Chemistry Research and Technologies, Lilly Corporate Center, Eli Lilly and Company, 893 S Delaware Street, Indianapolis, IN 46285 USA
| | - Mark J. Nilges
- />School of Molecular and Cellular Biology and Illinois EPR Research Center, Illinois EPR Research Center, 506 S. Mathews St., Urbana, IL 61801 USA
| | - David E. Timm
- />Discovery Chemistry Research and Technologies, Lilly Corporate Center, Eli Lilly and Company, 893 S Delaware Street, Indianapolis, IN 46285 USA
| | - Stephanie L. Stout
- />Discovery Chemistry Research and Technologies, Lilly Corporate Center, Eli Lilly and Company, 893 S Delaware Street, Indianapolis, IN 46285 USA
| | - William F. Matter
- />Division of Endocrine and Cardiovascular Research, Lilly Corporate Center, Eli Lilly and Company, 893 S Delaware Street, Indianapolis, IN 46285 USA
| | - Najia Jin
- />Division of Endocrine and Cardiovascular Research, Lilly Corporate Center, Eli Lilly and Company, 893 S Delaware Street, Indianapolis, IN 46285 USA
| | - Prabhakar K. Jadhav
- />Discovery Chemistry Research and Technologies, Lilly Corporate Center, Eli Lilly and Company, 893 S Delaware Street, Indianapolis, IN 46285 USA
| | - Gary G. Deng
- />Division of Endocrine and Cardiovascular Research, Lilly Corporate Center, Eli Lilly and Company, 893 S Delaware Street, Indianapolis, IN 46285 USA
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13
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Carson MW, Zhang J, Chalmers MJ, Bocchinfuso WP, Holifield KD, Masquelin T, Stites RE, Stayrook KR, Griffin PR, Dodge JA. HDX reveals unique fragment ligands for the vitamin D receptor. Bioorg Med Chem Lett 2014; 24:3459-63. [PMID: 24974344 DOI: 10.1016/j.bmcl.2014.05.070] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 05/16/2014] [Accepted: 05/20/2014] [Indexed: 11/30/2022]
Abstract
Modulation of the vitamin D receptor (VDR) with a ligand has the potential to be useful for the oral treatment of osteoporosis. One component of our lead generation strategy to identify synthetic ligands for VDR included a fragment based drug design approach. Screening of ligands in a VDR fluorescence polarization assay and a RXR/VDR conformation sensing assay resulted in the identification of multiple fragment hits (lean >0.30). These fragment scaffolds were subsequently evaluated for interaction with the VDR ligand binding domain using hydrogen-deuterium exchange (HDX) mass spectrometry. Significant protection of H/D exchange was observed for some fragments in helixes 3, 7, and 8 of the ligand binding domain, regions which are similar to those seen for the natural hormone VD3. The fragments appear to mimic the A-ring of VD3 thereby providing viable starting points for synthetic expansion.
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Affiliation(s)
- Matthew W Carson
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, United States.
| | - Jun Zhang
- Department of Molecular Therapeutics, United States
| | - Michael J Chalmers
- Department of Molecular Therapeutics, United States; The Scripps Research Molecular Screening Center (SRMSC), United States
| | - Wayne P Bocchinfuso
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, United States
| | - Karol D Holifield
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, United States
| | - Thierry Masquelin
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, United States
| | - Ryan E Stites
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, United States
| | - Keith R Stayrook
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, United States
| | - Patrick R Griffin
- Department of Molecular Therapeutics, United States; The Scripps Research Molecular Screening Center (SRMSC), United States
| | - Jeffery A Dodge
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, United States
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14
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Bryk R, Arango N, Maksymiuk C, Balakrishnan A, Wu YT, Wong CH, Masquelin T, Hipskind P, Lima CD, Nathan C. Lipoamide channel-binding sulfonamides selectively inhibit mycobacterial lipoamide dehydrogenase. Biochemistry 2013; 52:9375-84. [PMID: 24251446 DOI: 10.1021/bi401077f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tuberculosis remains a global health emergency that calls for treatment regimens directed at new targets. Here we explored lipoamide dehydrogenase (Lpd), a metabolic and detoxifying enzyme in Mycobacterium tuberculosis (Mtb) whose deletion drastically impairs Mtb's ability to establish infection in the mouse. Upon screening more than 1.6 million compounds, we identified N-methylpyridine 3-sulfonamides as potent and species-selective inhibitors of Mtb Lpd affording >1000-fold selectivity versus the human homologue. The sulfonamides demonstrated low nanomolar affinity and bound at the lipoamide channel in an Lpd-inhibitor cocrystal. Their selectivity could be attributed, at least partially, to hydrogen bonding of the sulfonamide amide oxygen with the species variant Arg93 in the lipoamide channel. Although potent and selective, the sulfonamides did not enter mycobacteria, as determined by their inability to accumulate in Mtb to effective levels or to produce changes in intracellular metabolites. This work demonstrates that high potency and selectivity can be achieved at the lipoamide-binding site of Mtb Lpd, a site different from the NAD⁺/NADH pocket targeted by previously reported species-selective triazaspirodimethoxybenzoyl inhibitors.
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Affiliation(s)
- Ruslana Bryk
- Department of Microbiology and Immunology and ‡Department of Pharmacology, Weill Cornell Medical College , New York, New York 10065, United States
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15
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Kumar A, Casey A, Odingo J, Kesicki EA, Abrahams G, Vieth M, Masquelin T, Mizrahi V, Hipskind PA, Sherman DR, Parish T. A high-throughput screen against pantothenate synthetase (PanC) identifies 3-biphenyl-4-cyanopyrrole-2-carboxylic acids as a new class of inhibitor with activity against Mycobacterium tuberculosis. PLoS One 2013; 8:e72786. [PMID: 24244263 PMCID: PMC3820577 DOI: 10.1371/journal.pone.0072786] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [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] [Received: 05/06/2013] [Accepted: 07/12/2013] [Indexed: 12/17/2022] Open
Abstract
The enzyme pantothenate synthetase, PanC, is an attractive drug target in Mycobacterium tuberculosis. It is essential for the in vitro growth of M. tuberculosis and for survival of the bacteria in the mouse model of infection. PanC is absent from mammals. We developed an enzyme-based assay to identify inhibitors of PanC, optimized it for high-throughput screening, and tested a large and diverse library of compounds for activity. Two compounds belonging to the same chemical class of 3-biphenyl-4- cyanopyrrole-2-carboxylic acids had activity against the purified recombinant protein, and also inhibited growth of live M. tuberculosis in manner consistent with PanC inhibition. Thus we have identified a new class of PanC inhibitors with whole cell activity that can be further developed.
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Affiliation(s)
- Anuradha Kumar
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
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16
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Godfrey AG, Masquelin T, Hemmerle H. A remote-controlled adaptive medchem lab: an innovative approach to enable drug discovery in the 21st Century. Drug Discov Today 2013; 18:795-802. [DOI: 10.1016/j.drudis.2013.03.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 02/25/2013] [Accepted: 03/08/2013] [Indexed: 10/27/2022]
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17
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Dreyfus N, Myers JK, Badescu VO, de Frutos O, de la Puente ML, Ding C, Filla SA, Fynboe K, Gernert DL, Heinz BA, Hemrick-Luecke SK, Johnson KW, Johnson MP, López P, Love PL, Martin LJ, Masquelin T, McCoy MJ, Mendiola J, Morrow D, Muhlhauser M, Pascual G, Perun TJ, Pfeifer LA, Phebus LA, Richards SJ, Rincón JA, Seest EP, Shah J, Shaojuan J, Simmons RMA, Stephenson GA, Tromiczak EG, Thompson LK, Walter MW, Weber WW, Zarrinmayeh H, Thomas CE, Joshi E, Iyengar S, Johansson AM. Discovery of a potent, dual serotonin and norepinephrine reuptake inhibitor. ACS Med Chem Lett 2013; 4:560-4. [PMID: 24900709 DOI: 10.1021/ml400049p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [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: 02/05/2013] [Accepted: 05/07/2013] [Indexed: 11/30/2022] Open
Abstract
The objective of the described research effort was to identify a novel serotonin and norepinephrine reuptake inhibitor (SNRI) with improved norepinephrine transporter activity and acceptable metabolic stability and exhibiting minimal drug-drug interaction. We describe herein the discovery of a series of 3-substituted pyrrolidines, exemplified by compound 1. Compound 1 is a selective SNRI in vitro and in vivo, has favorable ADME properties, and retains inhibitory activity in the formalin model of pain behavior. Compound 1 thus represents a potential new probe to explore utility of SNRIs in central nervous system disorders, including chronic pain conditions.
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Affiliation(s)
- Nicolas Dreyfus
- Research and Development, Eli Lilly and Company Ltd., Sunninghill Road, Windlesham,
Surrey GU20 6PH, United Kingdom
| | - Jason K. Myers
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Valentina O. Badescu
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Oscar de Frutos
- Lilly S.A., Centro de Investigación,
Avda. de la Industria, 30, Alcobendas-Madrid
28108, Spain
| | - Maria Luz de la Puente
- Lilly S.A., Centro de Investigación,
Avda. de la Industria, 30, Alcobendas-Madrid
28108, Spain
| | - Chunjin Ding
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Sandra A. Filla
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | | | - Douglas L. Gernert
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Beverly A. Heinz
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Susan K. Hemrick-Luecke
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Kirk W. Johnson
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Michael P. Johnson
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Pilar López
- Lilly S.A., Centro de Investigación,
Avda. de la Industria, 30, Alcobendas-Madrid
28108, Spain
| | | | - Laura J. Martin
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Thierry Masquelin
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Michael J. McCoy
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Javier Mendiola
- Lilly S.A., Centro de Investigación,
Avda. de la Industria, 30, Alcobendas-Madrid
28108, Spain
| | - Denise Morrow
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Mark Muhlhauser
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Gustavo Pascual
- Lilly S.A., Centro de Investigación,
Avda. de la Industria, 30, Alcobendas-Madrid
28108, Spain
| | - Thomas J. Perun
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Lance A. Pfeifer
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Lee A. Phebus
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Simon J. Richards
- Research and Development, Eli Lilly and Company Ltd., Sunninghill Road, Windlesham,
Surrey GU20 6PH, United Kingdom
| | - Juan Antonio Rincón
- Lilly S.A., Centro de Investigación,
Avda. de la Industria, 30, Alcobendas-Madrid
28108, Spain
| | - Eric P. Seest
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Jikesh Shah
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Jia Shaojuan
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Rosa Maria A. Simmons
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Gregory A. Stephenson
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Eric G. Tromiczak
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Linda K. Thompson
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Magnus W. Walter
- Research and Development, Eli Lilly and Company Ltd., Sunninghill Road, Windlesham,
Surrey GU20 6PH, United Kingdom
| | - Wayne W. Weber
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Hamideh Zarrinmayeh
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Craig E. Thomas
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Elizabeth Joshi
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Smriti Iyengar
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
| | - Anette M. Johansson
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis,
Indiana 46285, United States
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Bui H, Masquelin T, Perun T, Castle T, Dage J, Kuo MS. Investigation of retention behavior of drug molecules in supercritical fluid chromatography using linear solvation energy relationships. J Chromatogr A 2008; 1206:186-95. [DOI: 10.1016/j.chroma.2008.08.050] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 07/29/2008] [Accepted: 08/04/2008] [Indexed: 11/29/2022]
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Masquelin T, Bui H, Brickley B, Stephenson G, Schwerkoske J, Hulme C. Sequential Ugi/Strecker reactions via microwave assisted organic synthesis: novel 3-center-4-component and 3-center-5-component multi-component reactions. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2006.01.160] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Masquelin T, Broger E, Müller K, Schmid R, Obrecht D. Synthesis of Enantiomerically PureD- andL-(Heteroaryl)alanines by asymmetric hydrogenation of (Z)-α-amino-αβ-didehydro esters. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19940770518] [Citation(s) in RCA: 39] [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: 11/11/2022]
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Masquelin T, Graveleau N. Solid-Phase Synthesis of Pyrimido[4,5- d]pyrimidine-2,4(1 H,3 H)-diones. SYNTHESIS-STUTTGART 2003. [DOI: 10.1055/s-2003-40891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Masquelin T, Obrecht D. A new general three component solution-phase synthesis of 2-amino-1,3-thiazole and 2,4-diamino-1,3-thiazole combinatorial libraries. Tetrahedron 2001. [DOI: 10.1016/s0040-4020(00)01003-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [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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Abstract
A novel solid-phase synthesis of a 2,4-diaminothiazole library starting from a polymer-bound thiouronium salt is described. The synthetic strategy involves formation of polymer-bound thioureido-thiourea intermediates [5] which by treatment with alpha-bromo-ketones [6] undergoes S-alkylation, followed by a base-catalyzed intramolecular-ring closure/cleavage to give 2,4-diaminothiazoles [8]. This strategy tolerates a wide range of functionality and protecting groups. The novel feature of our method is a polymer-supported auto-scavenging strategy (PSAS), which provides a clean, high-yielding, and traceless synthesis to 2,4-diaminothiazoles.
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Affiliation(s)
- R Baer
- Department of Chemical Technologies, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
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Masquelin T, Sprenger D, Baer R, Gerber F, Mercadal Y. A Novel Solution- and Solid-Phase Approach to 2,4,5-tri- and 2,4,5,6-tetrasubstituted pyrimidines and their conversion into condensed heterocycles. Helv Chim Acta 1998. [DOI: 10.1002/hlca.19980810315] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Obrecht D, Gerber F, Sprengeir D, Masquelin T. A Novel Approach towards 2,3,5-Trisubstituted Thiophenesvia tandemMichael addition/intramolecularKnoevenagel condensation. Helv Chim Acta 1997. [DOI: 10.1002/hlca.19970800217] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Masquelin T, Hengartnerb U, Streith J. Naphthopyranquinone Antibiotics: Novel enantioselective syntheses of frenolicin B and some of its stereoisomers. Helv Chim Acta 1997. [DOI: 10.1002/hlca.19970800104] [Citation(s) in RCA: 27] [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: 11/09/2022]
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Chucholowski A, Masquelin T, Obrecht D, Stadlwieser J, Villalgordo JM. Novel Solution- and Solid-Phase Strategies for the Parallel and Combinatorial Synthesis of Small-Molecular-Weight Compound Libraries. Chimia (Aarau) 1996. [DOI: 10.2533/chimia.1996.525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In this account dedicated to '100 years Roche' in CHIMIA, we present some of our strategies towards the synthesis of interesting novel amino-acid-derived building blocks; multigeneration synthesis of thiazole libraries in solution; a novel solid-phase approach towards highly substituted pyrimidines using a novel safety-catch linker principle and a multidirectional cleavage procedure; a versatile solid-phase synthesis of quinazolones taking advantage of the Staudinger phosphorylimine chemistry combined with a novel cyclization and cleavage strategy, and finally a novel solid-phase diketopiperazine synthesis combining the Ugi four-component reaction with a final ring-forming cleavage step.
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