1
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Shin N, Stubbs M, Koblish H, Yue EW, Soloviev M, Douty B, Wang KH, Wang Q, Gao M, Feldman P, Yang G, Hall L, Hansbury M, O'Connor S, Leffet L, Collins R, Katiyar K, He X, Waeltz P, Collier P, Lu J, Li YL, Li Y, Liu PCC, Burn T, Covington M, Diamond S, Shuey D, Roberts A, Yeleswaram S, Hollis G, Metcalf B, Yao W, Huber R, Combs A, Newton R, Scherle P. Parsaclisib Is a Next-Generation Phosphoinositide 3-Kinase δ Inhibitor with Reduced Hepatotoxicity and Potent Antitumor and Immunomodulatory Activities in Models of B-Cell Malignancy. J Pharmacol Exp Ther 2020; 374:211-222. [PMID: 32345620 DOI: 10.1124/jpet.120.265538] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/20/2020] [Indexed: 12/18/2022] Open
Abstract
The clinical use of first-generation phosphoinositide 3-kinase (PI3K)δ inhibitors in B-cell malignancies is hampered by hepatotoxicity, requiring dose reduction, treatment interruption, and/or discontinuation of therapy. In addition, potential molecular mechanisms by which resistance to this class of drugs occurs have not been investigated. Parsaclisib (INCB050465) is a potent and selective next-generation PI3Kδ inhibitor that differs in structure from first-generation PI3Kδ inhibitors and has shown encouraging anti-B-cell tumor activity and reduced hepatotoxicity in phase 1/2 clinical studies. Here, we present preclinical data demonstrating parsaclisib as a potent inhibitor of PI3Kδ with over 1000-fold selectivity against other class 1 PI3K isozymes. Parsaclisib directly blocks PI3K signaling-mediated cell proliferation in B-cell lines in vitro and in vivo and indirectly controls tumor growth by lessening immunosuppression through regulatory T-cell inhibition in a syngeneic lymphoma model. Diffuse large B-cell lymphoma cell lines overexpressing MYC were insensitive to proliferation blockade via PI3Kδ signaling inhibition by parsaclisib, but their proliferative activities were reduced by suppression of MYC gene transcription. Molecular structure analysis of the first- and next-generation PI3Kδ inhibitors combined with clinical observation suggests that hepatotoxicity seen with the first-generation inhibitors could result from a structure-related off-target effect. Parsaclisib is currently being evaluated in multiple phase 2 clinical trials as a therapy against various hematologic malignancies of B-cell origin (NCT03126019, NCT02998476, NCT03235544, NCT03144674, and NCT02018861). SIGNIFICANCE STATEMENT: The preclinical properties described here provide the mechanism of action and support clinical investigations of parsaclisib as a therapy for B-cell malignancies. MYC overexpression was identified as a resistance mechanism to parsaclisib in DLBCL cells, which may be useful in guiding further translational studies for the selection of patients with DLBCL who might benefit from PI3Kδ inhibitor treatment in future trials. Hepatotoxicity associated with first-generation PI3Kδ inhibitors may be an off-target effect of that class of compounds.
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Affiliation(s)
- Niu Shin
- Incyte Research Institute, Wilmington, Delaware
| | | | | | - Eddy W Yue
- Incyte Research Institute, Wilmington, Delaware
| | | | - Brent Douty
- Incyte Research Institute, Wilmington, Delaware
| | | | - Qian Wang
- Incyte Research Institute, Wilmington, Delaware
| | | | | | | | - Leslie Hall
- Incyte Research Institute, Wilmington, Delaware
| | | | | | - Lynn Leffet
- Incyte Research Institute, Wilmington, Delaware
| | | | | | - Xin He
- Incyte Research Institute, Wilmington, Delaware
| | - Paul Waeltz
- Incyte Research Institute, Wilmington, Delaware
| | | | - Jin Lu
- Incyte Research Institute, Wilmington, Delaware
| | - Yun-Long Li
- Incyte Research Institute, Wilmington, Delaware
| | - Yanlong Li
- Incyte Research Institute, Wilmington, Delaware
| | | | | | | | | | - Dana Shuey
- Incyte Research Institute, Wilmington, Delaware
| | | | | | - Greg Hollis
- Incyte Research Institute, Wilmington, Delaware
| | | | - Wenqing Yao
- Incyte Research Institute, Wilmington, Delaware
| | - Reid Huber
- Incyte Research Institute, Wilmington, Delaware
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2
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Yue EW, Li YL, Douty B, He C, Mei S, Wayland B, Maduskuie T, Falahatpisheh N, Sparks RB, Polam P, Zhu W, Glenn J, Feng H, Zhang K, Li Y, He X, Katiyar K, Covington M, Feldman P, Shin N, Wang KH, Diamond S, Li Y, Koblish HK, Hall L, Scherle P, Yeleswaram S, Xue CB, Metcalf B, Combs AP, Yao W. INCB050465 (Parsaclisib), a Novel Next-Generation Inhibitor of Phosphoinositide 3-Kinase Delta (PI3Kδ). ACS Med Chem Lett 2019; 10:1554-1560. [PMID: 31749910 DOI: 10.1021/acsmedchemlett.9b00334] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/17/2019] [Indexed: 01/21/2023] Open
Abstract
A medicinal chemistry effort focused on identifying a structurally diverse candidate for phosphoinositide 3-kinase delta (PI3Kδ) led to the discovery of clinical candidate INCB050465 (20, parsaclisib). The unique structure of 20 contains a pyrazolopyrimidine hinge-binder in place of a purine motif that is present in other PI3Kδ inhibitors, such as idelalisib (1), duvelisib (2), and INCB040093 (3, dezapelisib). Parsaclisib (20) is a potent and highly selective inhibitor of PI3Kδ with drug-like ADME properties that exhibited an excellent in vivo profile as demonstrated through pharmacokinetic studies in rats, dogs, and monkeys and through pharmacodynamic and efficacy studies in a mouse Pfeiffer xenograft model.
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Affiliation(s)
- Eddy W. Yue
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Yun-Long Li
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Brent Douty
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Chunhong He
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Song Mei
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Brian Wayland
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Thomas Maduskuie
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Nikoo Falahatpisheh
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Richard B. Sparks
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Padmaja Polam
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Wenyu Zhu
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Joseph Glenn
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Hao Feng
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Ke Zhang
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Yanlong Li
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Xin He
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Kamna Katiyar
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Maryanne Covington
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Patricia Feldman
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Niu Shin
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Kathy He Wang
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Sharon Diamond
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Yu Li
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Holly K. Koblish
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Leslie Hall
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Peggy Scherle
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Swamy Yeleswaram
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Chu-Biao Xue
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Brian Metcalf
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Andrew P. Combs
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Wenqing Yao
- Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
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3
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Yue EW, Sparks R, Polam P, Modi D, Douty B, Wayland B, Glass B, Takvorian A, Glenn J, Zhu W, Bower M, Liu X, Leffet L, Wang Q, Bowman KJ, Hansbury MJ, Wei M, Li Y, Wynn R, Burn TC, Koblish HK, Fridman JS, Emm T, Scherle PA, Metcalf B, Combs AP. INCB24360 (Epacadostat), a Highly Potent and Selective Indoleamine-2,3-dioxygenase 1 (IDO1) Inhibitor for Immuno-oncology. ACS Med Chem Lett 2017; 8:486-491. [PMID: 28523098 PMCID: PMC5430407 DOI: 10.1021/acsmedchemlett.6b00391] [Citation(s) in RCA: 188] [Impact Index Per Article: 26.9] [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] [Received: 10/06/2016] [Accepted: 02/24/2017] [Indexed: 01/25/2023] Open
Abstract
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A data-centric medicinal
chemistry approach led to the invention
of a potent and selective IDO1 inhibitor 4f, INCB24360
(epacadostat). The molecular structure of INCB24360 contains several
previously unknown or underutilized functional groups in drug substances,
including a hydroxyamidine, furazan, bromide, and sulfamide. These
moieties taken together in a single structure afford a compound that
falls outside of “drug-like” space. Nevertheless, the in vitro ADME data is consistent with the good cell permeability
and oral bioavailability observed in all species (rat, dog, monkey)
tested. The extensive intramolecular hydrogen bonding observed in
the small molecule crystal structure of 4f is believed
to significantly contribute to the observed permeability and PK. Epacadostat
in combination with anti-PD1 mAb pembrolizumab is currently being
studied in a phase 3 clinical trial in patients with unresectable
or metastatic melanoma.
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Affiliation(s)
- Eddy W. Yue
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Richard Sparks
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Padmaja Polam
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Dilip Modi
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Brent Douty
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Brian Wayland
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Brian Glass
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Amy Takvorian
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Joseph Glenn
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Wenyu Zhu
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Michael Bower
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Xiangdong Liu
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Lynn Leffet
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Qian Wang
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Kevin J. Bowman
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Michael J. Hansbury
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Min Wei
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Yanlong Li
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Richard Wynn
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Timothy C. Burn
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Holly K. Koblish
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Jordan S. Fridman
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Tom Emm
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Peggy A. Scherle
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Brian Metcalf
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
| | - Andrew P. Combs
- Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States
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4
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Koblish HK, Hansbury MJ, Bowman KJ, Yang G, Neilan CL, Haley PJ, Burn TC, Waeltz P, Sparks RB, Yue EW, Combs AP, Scherle PA, Vaddi K, Fridman JS. Hydroxyamidine inhibitors of indoleamine-2,3-dioxygenase potently suppress systemic tryptophan catabolism and the growth of IDO-expressing tumors. Mol Cancer Ther 2010; 9:489-98. [PMID: 20124451 DOI: 10.1158/1535-7163.mct-09-0628] [Citation(s) in RCA: 202] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Malignant tumors arise, in part, because the immune system does not adequately recognize and destroy them. Expression of indoleamine-2,3-dioxygenase (IDO; IDO1), a rate-limiting enzyme in the catabolism of tryptophan into kynurenine, contributes to this immune evasion. Here we describe the effects of systemic IDO inhibition using orally active hydroxyamidine small molecule inhibitors. A single dose of INCB023843 or INCB024360 results in efficient and durable suppression of Ido1 activity in the plasma of treated mice and dogs, the former to levels seen in Ido1-deficient mice. Hydroxyamidines potently suppress tryptophan metabolism in vitro in CT26 colon carcinoma and PAN02 pancreatic carcinoma cells and in vivo in tumors and their draining lymph nodes. Repeated administration of these IDO1 inhibitors impedes tumor growth in a dose- and lymphocyte-dependent fashion and is well tolerated in efficacy and preclinical toxicology studies. Substantiating the fundamental role of tumor cell-derived IDO expression, hydroxyamidines control the growth of IDO-expressing tumors in Ido1-deficient mice. These activities can be attributed, at least partially, to the increased immunoreactivity of lymphocytes found in tumors and their draining lymph nodes and to the reduction in tumor-associated regulatory T cells. INCB024360, a potent IDO1 inhibitor with desirable pharmaceutical properties, is poised to start clinical trials in cancer patients.
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Affiliation(s)
- Holly K Koblish
- Preclinical Biology, Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, DE 19880, USA.
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5
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Hartz RA, Ahuja VT, Rafalski M, Schmitz WD, Brenner AB, Denhart DJ, Ditta JL, Deskus JA, Yue EW, Arvanitis AG, Lelas S, Li YW, Molski TF, Wong H, Grace JE, Lentz KA, Li J, Lodge NJ, Zaczek R, Combs AP, Olson RE, Mattson RJ, Bronson JJ, Macor JE. Corrections to In Vitro Intrinsic Clearance-Based Optimization of N3-Phenylpyrazinones as Corticotropin-Releasing Factor-1 (CRF 1) Receptor Antagonists. J Med Chem 2009. [DOI: 10.1021/jm9011033] [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: 11/28/2022]
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6
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Hartz RA, Ahuja VT, Arvanitis AG, Rafalski M, Yue EW, Denhart DJ, Schmitz WD, Ditta JL, Deskus JA, Brenner AB, Hobbs FW, Payne J, Lelas S, Li YW, Molski TF, Mattson GK, Peng Y, Wong H, Grace JE, Lentz KA, Qian-Cutrone J, Zhuo X, Shu YZ, Lodge NJ, Zaczek R, Combs AP, Olson RE, Bronson JJ, Mattson RJ, Macor JE. Synthesis, structure-activity relationships, and in vivo evaluation of N3-phenylpyrazinones as novel corticotropin-releasing factor-1 (CRF1) receptor antagonists. J Med Chem 2009; 52:4173-91. [PMID: 19552437 DOI: 10.1021/jm900301y] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Evidence suggests that corticotropin-releasing factor-1 (CRF(1)) receptor antagonists may offer therapeutic potential for the treatment of diseases associated with elevated levels of CRF such as anxiety and depression. A pyrazinone-based chemotype of CRF(1) receptor antagonists was discovered. Structure-activity relationship studies led to the identification of numerous potent analogues including 12p, a highly potent and selective CRF(1) receptor antagonist with an IC(50) value of 0.26 nM. The pharmacokinetic properties of 12p were assessed in rats and Cynomolgus monkeys. Compound 12p was efficacious in the defensive withdrawal test (an animal model of anxiety) in rats. The synthesis, structure-activity relationships and in vivo properties of compounds within the pyrazinone chemotype are described.
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Affiliation(s)
- Richard A Hartz
- Research and Development, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492, USA.
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7
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Hartz RA, Ahuja VT, Rafalski M, Schmitz WD, Brenner AB, Denhart DJ, Ditta JL, Deskus JA, Yue EW, Arvanitis AG, Lelas S, Li YW, Molski TF, Wong H, Grace JE, Lentz KA, Li J, Lodge NJ, Zaczek R, Combs AP, Olson RE, Mattson RJ, Bronson JJ, Macor JE. In Vitro Intrinsic Clearance-Based Optimization of N3-Phenylpyrazinones as Corticotropin-Releasing Factor-1 (CRF1) Receptor Antagonists. J Med Chem 2009; 52:4161-72. [DOI: 10.1021/jm900302q] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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Yue EW, Douty B, Wayland B, Bower M, Liu X, Leffet L, Wang Q, Bowman KJ, Hansbury MJ, Liu C, Wei M, Li Y, Wynn R, Burn TC, Koblish HK, Fridman JS, Metcalf B, Scherle PA, Combs AP. Discovery of Potent Competitive Inhibitors of Indoleamine 2,3-Dioxygenase with in Vivo Pharmacodynamic Activity and Efficacy in a Mouse Melanoma Model. J Med Chem 2009; 52:7364-7. [DOI: 10.1021/jm900518f] [Citation(s) in RCA: 185] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Eddy W. Yue
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
| | - Brent Douty
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
| | - Brian Wayland
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
| | - Michael Bower
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
| | - Xiangdong Liu
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
| | - Lynn Leffet
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
| | - Qian Wang
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
| | - Kevin J. Bowman
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
| | - Michael J. Hansbury
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
| | - Changnian Liu
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
| | - Min Wei
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
| | - Yanlong Li
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
| | - Richard Wynn
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
| | - Timothy C. Burn
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
| | - Holly K. Koblish
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
| | - Jordan S. Fridman
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
| | - Brian Metcalf
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
| | - Peggy A. Scherle
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
| | - Andrew P. Combs
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880
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9
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Douty B, Wayland B, Ala PJ, Bower MJ, Pruitt J, Bostrom L, Wei M, Klabe R, Gonneville L, Wynn R, Burn TC, Liu PC, Combs AP, Yue EW. Isothiazolidinone inhibitors of PTP1B containing imidazoles and imidazolines. Bioorg Med Chem Lett 2008; 18:66-71. [DOI: 10.1016/j.bmcl.2007.11.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2007] [Revised: 10/31/2007] [Accepted: 11/06/2007] [Indexed: 12/01/2022]
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10
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Ala PJ, Gonneville L, Hillman M, Becker-Pasha M, Yue EW, Douty B, Wayland B, Polam P, Crawley ML, McLaughlin E, Sparks RB, Glass B, Takvorian A, Combs AP, Burn TC, Hollis GF, Wynn R. Structural Insights into the Design of Nonpeptidic Isothiazolidinone-containing Inhibitors of Protein-tyrosine Phosphatase 1B. J Biol Chem 2006; 281:38013-21. [PMID: 17028182 DOI: 10.1074/jbc.m607913200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Structural analyses of the protein-tyrosine phosphatase 1B (PTP1B) active site and inhibitor complexes have aided in optimization of a peptide inhibitor containing the novel (S)-isothiazolidinone (IZD) phosphonate mimetic. Potency and permeability were simultaneously improved by replacing the polar peptidic backbone of the inhibitor with nonpeptidic moieties. The C-terminal primary amide was replaced with a benzimidazole ring, which hydrogen bonds to the carboxylate of Asp(48), and the N terminus of the peptide was replaced with an aryl sulfonamide, which hydrogen bonds to Asp(48) and the backbone NH of Arg(47) via a water molecule. Although both substituents retain the favorable hydrogen bonding network of the peptide scaffold, their aryl rings interact weakly with the protein. The aryl ring of benzimidazole is partially solvent exposed and only participates in van der Waals interactions with Phe(182) of the flap. The aryl ring of aryl sulfonamide adopts an unexpected conformation and only participates in intramolecular pi-stacking interactions with the benzimidazole ring. These results explain the flat SAR for substitutions on both rings and the reason why unsubstituted moieties were selected as candidates. Finally, substituents ortho to the IZD heterocycle on the aryl ring of the IZD-phenyl moiety bind in a small narrow site adjacent to the primary phosphate binding pocket. The crystal structure of an o-chloro derivative reveals that chlorine interacts extensively with residues in the small site. The structural insights that have led to the discovery of potent benzimidazole aryl sulfonamide o-substituted derivatives are discussed in detail.
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Affiliation(s)
- Paul J Ala
- Incyte Corporation, Wilmington, Delaware 19880, USA.
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11
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Yue EW, Wayland B, Douty B, Crawley ML, McLaughlin E, Takvorian A, Wasserman Z, Bower MJ, Wei M, Li Y, Ala PJ, Gonneville L, Wynn R, Burn TC, Liu PCC, Combs AP. Isothiazolidinone heterocycles as inhibitors of protein tyrosine phosphatases: Synthesis and structure–activity relationships of a peptide scaffold. Bioorg Med Chem 2006; 14:5833-49. [PMID: 16769216 DOI: 10.1016/j.bmc.2006.05.032] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [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: 04/24/2006] [Accepted: 05/15/2006] [Indexed: 01/18/2023]
Abstract
The structure-based design and discovery of the isothiazolidinone (IZD) heterocycle as a mimic of phosphotyrosine (pTyr) has led to the identification of novel IZD-containing inhibitors of protein tyrosine phosphatase 1B (PTP1B). The structure-activity relationships (SARs) of peptidic IZD-containing inhibitors of PTP1B are described along with a novel synthesis of the aryl-IZD fragments via a Suzuki coupling. The SAR revealed the saturated IZD heterocycle (42) is the most potent heterocyclic pTyr mimetic compared to the unsaturated IZD (25), the thiadiazolidinone (TDZ) (38), and the regioisomeric unsaturated IZD (31). The X-ray crystal structures of 11c and 25 complexed with PTP1B were solved and revealed nearly identical binding interactions in the active site. Ab initio calculations effectively explain the strong binding of the (S)-IZD due to the preorganized binding of the IZD in its low energy conformation.
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Affiliation(s)
- Eddy W Yue
- Incyte Corporation, Discovery Chemistry, Experimental Station, Route 141, Henry Clay Road, Wilmington, DE 19880, USA.
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12
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Ala PJ, Gonneville L, Hillman MC, Becker-Pasha M, Wei M, Reid BG, Klabe R, Yue EW, Wayland B, Douty B, Polam P, Wasserman Z, Bower M, Combs AP, Burn TC, Hollis GF, Wynn R. Structural basis for inhibition of protein-tyrosine phosphatase 1B by isothiazolidinone heterocyclic phosphonate mimetics. J Biol Chem 2006; 281:32784-95. [PMID: 16916797 DOI: 10.1074/jbc.m606873200] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [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: 12/21/2022] Open
Abstract
Crystal structures of protein-tyrosine phosphatase 1B in complex with compounds bearing a novel isothiazolidinone (IZD) heterocyclic phosphonate mimetic reveal that the heterocycle is highly complementary to the catalytic pocket of the protein. The heterocycle participates in an extensive network of hydrogen bonds with the backbone of the phosphate-binding loop, Phe(182) of the flap, and the side chain of Arg(221). When substituted with a phenol, the small inhibitor induces the closed conformation of the protein and displaces all waters in the catalytic pocket. Saturated IZD-containing peptides are more potent inhibitors than unsaturated analogs because the IZD heterocycle and phenyl ring directly attached to it bind in a nearly orthogonal orientation with respect to each other, a conformation that is close to the energy minimum of the saturated IZD-phenyl moiety. These results explain why the heterocycle is a potent phosphonate mimetic and an ideal starting point for designing small nonpeptidic inhibitors.
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Affiliation(s)
- Paul J Ala
- Incyte Corporation, Experimental Station, Route 141 and Henry Clay Road, Wilmington, DE 19880, USA.
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13
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Combs AP, Zhu W, Crawley ML, Glass B, Polam P, Sparks RB, Modi D, Takvorian A, McLaughlin E, Yue EW, Wasserman Z, Bower M, Wei M, Rupar M, Ala PJ, Reid BM, Ellis D, Gonneville L, Emm T, Taylor N, Yeleswaram S, Li Y, Wynn R, Burn TC, Hollis G, Liu PCC, Metcalf B. Potent Benzimidazole Sulfonamide Protein Tyrosine Phosphatase 1B Inhibitors Containing the Heterocyclic (S)-Isothiazolidinone Phosphotyrosine Mimetic. J Med Chem 2006; 49:3774-89. [PMID: 16789735 DOI: 10.1021/jm0600904] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [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: 11/28/2022]
Abstract
Potent nonpeptidic benzimidazole sulfonamide inhibitors of protein tyrosine phosphatase 1B (PTP1B) were derived from the optimization of a tripeptide containing the novel (S)-isothiazolidinone ((S)-IZD) phosphotyrosine (pTyr) mimetic. An X-ray cocrystal structure of inhibitor 46/PTP1B at 1.8 A resolution demonstrated that the benzimidazole sulfonamides form a bidentate H bond to Asp48 as designed, although the aryl group of the sulfonamide unexpectedly interacts intramolecularly in a pi-stacking manner with the benzimidazole. The ortho substitution to the (S)-IZD on the aryl ring afforded low nanomolar enzyme inhibitors of PTP1B that also displayed low caco-2 permeability and cellular activity in an insulin receptor (IR) phosphorylation assay and an Akt phosphorylation assay. The design, synthesis, and SAR of this novel series of benzimidazole sulfonamide containing (S)-IZD inhibitors of PTP1B are presented herein.
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Affiliation(s)
- Andrew P Combs
- Incyte Corporation, Discovery Chemistry, Applied Technology, and Drug Metabolism, Experimental Station, Route 141 and Henry Clay Road, Wilmington, Delaware 19880, USA.
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14
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Combs AP, Yue EW, Bower M, Ala PJ, Wayland B, Douty B, Takvorian A, Polam P, Wasserman Z, Zhu W, Crawley ML, Pruitt J, Sparks R, Glass B, Modi D, McLaughlin E, Bostrom L, Li M, Galya L, Blom K, Hillman M, Gonneville L, Reid BG, Wei M, Becker-Pasha M, Klabe R, Huber R, Li Y, Hollis G, Burn TC, Wynn R, Liu P, Metcalf B. Structure-Based Design and Discovery of Protein Tyrosine Phosphatase Inhibitors Incorporating Novel Isothiazolidinone Heterocyclic Phosphotyrosine Mimetics. J Med Chem 2005; 48:6544-8. [PMID: 16220970 DOI: 10.1021/jm0504555] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [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
Structure-based design led to the discovery of novel (S)-isothiazolidinone ((S)-IZD) heterocyclic phosphotyrosine (pTyr) mimetics that when incorporated into dipeptides are exceptionally potent, competitive, and reversible inhibitors of protein tyrosine phosphatase 1B (PTP1B). The crystal structure of PTP1B in complex with our most potent inhibitor 12 revealed that the (S)-IZD heterocycle interacts extensively with the phosphate binding loop precisely as designed in silico. Our data provide strong evidence that the (S)-IZD is the most potent pTyr mimetic reported to date.
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Affiliation(s)
- Andrew P Combs
- Discovery Chemistry, Incyte Corporation, Experimental Station, E336/132A, Route 141 and Henry Clay Road, Wilmington, DE 19880, USA.
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15
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Yue EW, DiMeo SV, Higley CA, Markwalder JA, Burton CR, Benfield PA, Grafstrom RH, Cox S, Muckelbauer JK, Smallwood AM, Chen H, Chang CH, Trainor GL, Seitz SP. Synthesis and evaluation of indenopyrazoles as cyclin-dependent kinase inhibitors. Part 4: Heterocycles at C3. Bioorg Med Chem Lett 2004; 14:343-6. [PMID: 14698155 DOI: 10.1016/j.bmcl.2003.11.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [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: 11/16/2022]
Abstract
New indeno[1,2-c]pyrazol-4-one cyclin dependent kinase inhibitors have been disclosed. The most promising compounds are nanomolar enzyme inhibitors with excellent activity against tumor cells. The most advanced compound retains cell culture activity even in the presence of human serum proteins. The most advanced compound did not kill the normal fibroblast line AG1523.
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Affiliation(s)
- Eddy W Yue
- Bristol-Myers Squibb Company, Experimental Station, PO Box 80500, Wilmington, DE 19880-0500, USA.
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16
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Yue EW, Higley CA, DiMeo SV, Carini DJ, Nugiel DA, Benware C, Benfield PA, Burton CR, Cox S, Grafstrom RH, Sharp DM, Sisk LM, Boylan JF, Muckelbauer JK, Smallwood AM, Chen H, Chang CH, Seitz SP, Trainor GL. Synthesis and evaluation of indenopyrazoles as cyclin-dependent kinase inhibitors. 3. Structure activity relationships at C3(1,2). J Med Chem 2002; 45:5233-48. [PMID: 12431051 DOI: 10.1021/jm0201722] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [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: 11/28/2022]
Abstract
The identification of indeno[1,2-c]pyrazol-4-ones as inhibitors of cyclin-dependent kinases (CDKs) has led to the discovery of a series of novel and potent compounds. Herein, we report the effects of substitutions at C3 of the indeno[1,2-c]pyrazol-4-one core with alkyls, heterocycles, and substituted phenyls. Substitutions at the para position of the phenyl ring at C3 were generally well-tolerated; however, larger groups were generally inactive. For alkyls directly attached to C3, longer chain substituents were not tolerated; however, shorter alkyl groups and cyclic alkyls were acceptable. In general, the heterocycles at C3 gave the most potent analogues. One such heterocycle, 24j, was examined in detail and was determined to have a biological profile consistent with CDK inhibition. An X-ray crystal structure of one of the alkyl compounds, 13q, complexed with CDK2 was determined and showed the inhibitor residing in the adenosine 5'-triphosphate pocket of the enzyme.
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Affiliation(s)
- Eddy W Yue
- Bristol-Myers Squibb Company, Experimental Station, P.O. Box 80500, Wilmington, Delaware 19880-0500, USA.
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17
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18
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Nicolaou KC, Yue EW, la Greca S, Nadin A, Yang Z, Leresche JE, Tsuri T, Naniwa Y, de Riccardis F. Synthesis of Zaragozic Acid A/Squalestatin S1. Chemistry 1995. [DOI: 10.1002/chem.19950010712] [Citation(s) in RCA: 85] [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: 11/08/2022]
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19
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Nicolaou KC, Yue EW, Naniwa Y, De Riccardis F, Nadin A, Leresche JE, La Greca S, Yang Z. Zaragozic Acid A/Squalestatin S1: Synthetic and Retrosynthetic Studies. ACTA ACUST UNITED AC 1994. [DOI: 10.1002/anie.199421841] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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20
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Nicolaou KC, Nadin A, Leresche JE, Greca SL, Tsuri T, Yue EW, Yang Z. Synthesis of the First Fully Functionalized Core of the Zaragozic Acids/Squalestatins. ACTA ACUST UNITED AC 1994. [DOI: 10.1002/anie.199421871] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [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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21
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22
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23
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Nicolaou KC, Nadin A, Leresche JE, La Greca S, Tsuri T, Yue EW, Yang Z. Synthese des ersten vollständig funktionalisierten Gerüstes der Saragossasäuren/Squalestatine. Angew Chem Int Ed Engl 1994. [DOI: 10.1002/ange.19941062128] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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Nicolaou KC, Yue EW, Naniwa Y, De Riccardis F, Nadin A, Leresche JE, La Greca S, Yang Z. Saragossasäure A/Squalestatin S1: synthetische und retrosynthetische Untersuchungen. Angew Chem Int Ed Engl 1994. [DOI: 10.1002/ange.19941062127] [Citation(s) in RCA: 20] [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: 11/12/2022]
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25
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Abstract
Ever since the initial reports of the enediyne anticancer antibiotics in the late 1980s, researchers from a number of disciplines have been devoting increasing attention to their chemistry, biology, and potential medical applications. Synthetic chemists and molecular designers have been engaged in attempts to synthesize these molecules and to model their unique architecture. Considerable efforts have been directed at understanding and mimicking the various processes involved in the targeting, activation, and DNA cleavage associated with these natural products. This review summarizes the main contributions to the field, with particular emphasis on work from our laboratories. Highlights include studies of the Bergman reaction, which is central to the mechanism of action of enediynes, the design and chemical synthesis of a number of these systems, and biological studies with selected molecules. Finally, the total synthesis of calicheamicin gamma 1I, the most prominent member of this class of naturally occurring compounds, is discussed.
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry, Scripps Research Institute, La Jolla, CA 92037
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