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Van de Poël A, Toledo-Sherman L, Breccia P, Cachope R, Bate JR, Angulo-Herrera I, Wishart G, Matthews KL, Martin SL, Peacock M, Barnard A, Cox HC, Jones G, McAllister G, Vater H, Esmieu W, Clissold C, Lamers M, Leonard P, Jarvis RE, Blackaby W, Eznarriaga M, Lazari O, Yates D, Rose M, Jang SW, Muñoz-Sanjuan I, Dominguez C. Structure-Based Exploration of Selectivity for ATM Inhibitors in Huntington's Disease. J Med Chem 2021; 64:5018-5036. [PMID: 33783225 DOI: 10.1021/acs.jmedchem.1c00114] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Our group has recently shown that brain-penetrant ataxia telangiectasia-mutated (ATM) kinase inhibitors may have potential as novel therapeutics for the treatment of Huntington's disease (HD). However, the previously described pyranone-thioxanthenes (e.g., 4) failed to afford selectivity over a vacuolar protein sorting 34 (Vps34) kinase, an important kinase involved with autophagy. Given that impaired autophagy has been proposed as a pathogenic mechanism of neurodegenerative diseases such as HD, achieving selectivity over Vps34 became an important objective for our program. Here, we report the successful selectivity optimization of ATM over Vps34 by using X-ray crystal structures of a Vps34-ATM protein chimera where the Vps34 ATP-binding site was mutated to approximate that of an ATM kinase. The morpholino-pyridone and morpholino-pyrimidinone series that resulted as a consequence of this selectivity optimization process have high ATM potency and good oral bioavailability and have lower molecular weight, reduced lipophilicity, higher aqueous solubility, and greater synthetic tractability compared to the pyranone-thioxanthenes.
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Affiliation(s)
| | - Leticia Toledo-Sherman
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Perla Breccia
- Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Roger Cachope
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Jennifer R Bate
- Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | | | - Grant Wishart
- Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Kim L Matthews
- Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Sarah L Martin
- Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Marcus Peacock
- Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Amy Barnard
- Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Helen C Cox
- Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Graham Jones
- Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - George McAllister
- Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Huw Vater
- Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - William Esmieu
- Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Cole Clissold
- Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Marieke Lamers
- Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Philip Leonard
- Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Rebecca E Jarvis
- Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Wesley Blackaby
- Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Maria Eznarriaga
- Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Ovadia Lazari
- Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Dawn Yates
- Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Mark Rose
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Sung-Wook Jang
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Ignacio Muñoz-Sanjuan
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
| | - Celia Dominguez
- CHDI Management/CHDI Foundation, 6080 Center Drive, Los Angeles, California 90045, United States
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Non-regioselective functionalization: an underestimate chemical diversity generator in medicinal chemistry. Future Med Chem 2021; 13:595-599. [PMID: 33657835 DOI: 10.4155/fmc-2021-0011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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3
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Gagic Z, Ruzic D, Djokovic N, Djikic T, Nikolic K. In silico Methods for Design of Kinase Inhibitors as Anticancer Drugs. Front Chem 2020; 7:873. [PMID: 31970149 PMCID: PMC6960140 DOI: 10.3389/fchem.2019.00873] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 12/04/2019] [Indexed: 12/11/2022] Open
Abstract
Rational drug design implies usage of molecular modeling techniques such as pharmacophore modeling, molecular dynamics, virtual screening, and molecular docking to explain the activity of biomolecules, define molecular determinants for interaction with the drug target, and design more efficient drug candidates. Kinases play an essential role in cell function and therefore are extensively studied targets in drug design and discovery. Kinase inhibitors are clinically very important and widely used antineoplastic drugs. In this review, computational methods used in rational drug design of kinase inhibitors are discussed and compared, considering some representative case studies.
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Affiliation(s)
- Zarko Gagic
- Department of Pharmaceutical Chemistry, Faculty of Medicine, University of Banja Luka, Banja Luka, Bosnia and Herzegovina
| | - Dusan Ruzic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Nemanja Djokovic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Teodora Djikic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
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4
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Miller MS, Thompson PE, Gabelli SB. Structural Determinants of Isoform Selectivity in PI3K Inhibitors. Biomolecules 2019; 9:biom9030082. [PMID: 30813656 PMCID: PMC6468644 DOI: 10.3390/biom9030082] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/21/2019] [Indexed: 01/17/2023] Open
Abstract
Phosphatidylinositol 3-kinases (PI3Ks) are important therapeutic targets for the treatment of cancer, thrombosis, and inflammatory and immune diseases. The four highly homologous Class I isoforms, PI3K, PI3K, PI3K and PI3K have unique, non-redundant physiological roles and as such, isoform selectivity has been a key consideration driving inhibitor design and development. In this review, we discuss the structural biology of PI3Ks and how our growing knowledge of structure has influenced the medicinal chemistry of PI3K inhibitors. We present an analysis of the available structure-selectivity-activity relationship data to highlight key insights into how the various regions of the PI3K binding site influence isoform selectivity. The picture that emerges is one that is far from simple and emphasizes the complex nature of protein-inhibitor binding, involving protein flexibility, energetics, water networks and interactions with non-conserved residues.
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Affiliation(s)
- Michelle S Miller
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria 3052, Australia.
| | - Sandra B Gabelli
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
- Departments of Medicine, Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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5
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Garces AE, Stocks MJ. Class 1 PI3K Clinical Candidates and Recent Inhibitor Design Strategies: A Medicinal Chemistry Perspective. J Med Chem 2018; 62:4815-4850. [DOI: 10.1021/acs.jmedchem.8b01492] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Aimie E. Garces
- Centre for Biomolecular Sciences, University Park Nottingham, Nottingham NG7 2RD, U.K
| | - Michael J. Stocks
- Centre for Biomolecular Sciences, University Park Nottingham, Nottingham NG7 2RD, U.K
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Khil’ AM, Garmash NY, Kaminskii VA. New tetrasubstituted isonicotinic acid derivatives based on malononitrile. Reactions of sodium 2,6-diamino-3,5-dicyanopyridine-4-carboxylate. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1070428016090244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Exploring the isoform selectivity of TGX-221 related pyrido[1,2-a]pyrimidinone-based Class IA PI 3-kinase inhibitors: Synthesis, biological evaluation and molecular modelling. Bioorg Med Chem 2015; 23:3796-808. [DOI: 10.1016/j.bmc.2015.03.073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 03/26/2015] [Accepted: 03/28/2015] [Indexed: 01/24/2023]
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8
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Zhou W, Huang A, Zhang Y, Lin Q, Guo W, You Z, Yi Z, Liu M, Chen Y. Design and optimization of hybrid of 2,4-diaminopyrimidine and arylthiazole scaffold as anticancer cell proliferation and migration agents. Eur J Med Chem 2015; 96:269-80. [DOI: 10.1016/j.ejmech.2015.04.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/08/2015] [Accepted: 04/10/2015] [Indexed: 11/26/2022]
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9
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Hubbard PA, Moody CL, Murali R. Allosteric modulation of Ras and the PI3K/AKT/mTOR pathway: emerging therapeutic opportunities. Front Physiol 2014; 5:478. [PMID: 25566081 PMCID: PMC4267178 DOI: 10.3389/fphys.2014.00478] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 11/23/2014] [Indexed: 12/24/2022] Open
Abstract
GTPases and kinases are two predominant signaling modules that regulate cell fate. Dysregulation of Ras, a GTPase, and the three eponymous kinases that form key nodes of the associated phosphatidylinositol 4,5-bisphosphate 3-kinase (PI3K)/AKT/mTOR pathway have been implicated in many cancers, including pancreatic cancer, a disease noted for its current lack of effective therapeutics. The K-Ras isoform of Ras is mutated in over 90% of pancreatic ductal adenocarcinomas (PDAC) and there is growing evidence linking aberrant PI3K/AKT/mTOR pathway activity to PDAC. Although these observations suggest that targeting one of these nodes might lead to more effective treatment options for patients with pancreatic and other cancers, the complex regulatory mechanisms and the number of sequence-conserved isoforms of these proteins have been viewed as significant barriers in drug development. Emerging insights into the allosteric regulatory mechanisms of these proteins suggest novel opportunities for development of selective allosteric inhibitors with fragment-based drug discovery (FBDD) helping make significant inroads. The fact that allosteric inhibitors of Ras and AKT are currently in pre-clinical development lends support to this approach. In this article, we will focus on the recent advances and merits of developing allosteric drugs targeting these two inter-related signaling pathways.
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Affiliation(s)
- Paul A Hubbard
- Department of Biomedical Sciences, Cedars-Sinai Medical Center Los Angeles, CA, USA
| | - Colleen L Moody
- Department of Biomedical Sciences, Cedars-Sinai Medical Center Los Angeles, CA, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Cedars-Sinai Medical Center Los Angeles, CA, USA ; Department of Pathology and Laboratory Medicine, University of Pennsylvania Philadelphia, PA, USA
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Andrs M, Korabecny J, Jun D, Hodny Z, Bartek J, Kuca K. Phosphatidylinositol 3-Kinase (PI3K) and phosphatidylinositol 3-kinase-related kinase (PIKK) inhibitors: importance of the morpholine ring. J Med Chem 2014; 58:41-71. [PMID: 25387153 DOI: 10.1021/jm501026z] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Phosphatidylinositol 3-kinases (PI3Ks) and phosphatidylinositol 3-kinase-related protein kinases (PIKKs) are two related families of kinases that play key roles in regulation of cell proliferation, metabolism, migration, survival, and responses to diverse stresses including DNA damage. To design novel efficient strategies for treatment of cancer and other diseases, these kinases have been extensively studied. Despite their different nature, these two kinase families have related origin and share very similar kinase domains. Therefore, chemical inhibitors of these kinases usually carry analogous structural motifs. The most common feature of these inhibitors is a critical hydrogen bond to morpholine oxygen, initially present in the early nonspecific PI3K and PIKK inhibitor 3 (LY294002), which served as a valuable chemical tool for development of many additional PI3K and PIKK inhibitors. While several PI3K pathway inhibitors have recently shown promising clinical responses, inhibitors of the DNA damage-related PIKKs remain thus far largely in preclinical development.
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Affiliation(s)
- Martin Andrs
- Biomedical Research Center, University Hospital Hradec Kralove , Sokolska 81, 500 05 Hradec Kralove, Czech Republic
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Giordanetto F, Barlaam B, Berglund S, Edman K, Karlsson O, Lindberg J, Nylander S, Inghardt T. Discovery of 9-(1-phenoxyethyl)-2-morpholino-4-oxo-pyrido[1,2-a]pyrimidine-7-carboxamides as oral PI3Kβ inhibitors, useful as antiplatelet agents. Bioorg Med Chem Lett 2014; 24:3936-43. [DOI: 10.1016/j.bmcl.2014.07.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/01/2014] [Accepted: 07/02/2014] [Indexed: 12/15/2022]
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12
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Discovery of 9-(1-anilinoethyl)-2-morpholino-4-oxo-pyrido[1,2-a]pyrimidine-7-carboxamides as PI3Kβ/δ inhibitors for the treatment of PTEN-deficient tumours. Bioorg Med Chem Lett 2014; 24:3928-35. [DOI: 10.1016/j.bmcl.2014.06.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 06/11/2014] [Accepted: 06/13/2014] [Indexed: 12/14/2022]
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13
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Yang HL, Fang F, Zhao CP, Li DD, Li JR, Sun J, Du QR, Zhu HL. Design and synthesis of a novel series of N,4-diphenylpyrimidin-2-amine derivatives as potent and selective PI3Kγ inhibitors. MEDCHEMCOMM 2014. [DOI: 10.1039/c3md00301a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Twenty-one novelN,4-diphenylpyrimidin-2-amine derivatives have been synthesized as PI3Kγ selective inhibitors and compoundC8demonstrated the most potent inhibitory activity against PI3Kγ kinase.
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Affiliation(s)
- Hua-Lin Yang
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing, P. R. China
| | - Fei Fang
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing, P. R. China
| | - Chang-Po Zhao
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing, P. R. China
| | - Dong-Dong Li
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing, P. R. China
| | - Jing-Ran Li
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing, P. R. China
| | - Jian Sun
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing, P. R. China
| | - Qian-Ru Du
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing, P. R. China
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology
- Nanjing University
- Nanjing, P. R. China
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Krawczyk J, Keane N, Swords R, O'Dwyer M, Freeman CL, Giles FJ. Perifosine--a new option in treatment of acute myeloid leukemia? Expert Opin Investig Drugs 2013; 22:1315-27. [PMID: 23931614 DOI: 10.1517/13543784.2013.826648] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
INTRODUCTION Perifosine is a novel targeted oral Akt inhibitor. In preclinical leukemia models, perifosine has an independent cytotoxic potential but also synergizes well with other rationally selected targeted agents. The evidence from clinical trials supporting the use of perifosine in the therapy of leukemias is limited. The optimal dose and schedule have yet to be defined. However, given its favorable toxicity profile and mechanism of action, the therapeutic potential of perifosine should be evaluated in well-designed clinical trials. AREAS COVERED The role of the phosphatidylinositol-3 kinase (PI3K)/Akt zpathway in normal cells, cancer and leukemias is discussed. The mechanism of action of perifosine and the basic information on the development and chemical properties are summarized. The evidence from in vivo and in vitro studies is presented. The efficacy and side effect profile are summarized. EXPERT OPINION The safety and tolerability profile of perifosine are satisfactory. The evidence from clinical trials in patients with leukemias is very limited. The preclinical data are encouraging. Perifosine has the potential to play a role in the treatment of leukemias in the future. Its role needs to be confirmed in clinical trials.
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Welker ME, Kulik G. Recent syntheses of PI3K/Akt/mTOR signaling pathway inhibitors. Bioorg Med Chem 2013; 21:4063-91. [PMID: 23735831 PMCID: PMC3711139 DOI: 10.1016/j.bmc.2013.04.083] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 04/30/2013] [Indexed: 12/20/2022]
Abstract
This review focuses on the syntheses of PI3K/Akt/mTOR inhibitors that have been reported outside of the patent literature in the last 5years but is largely centered on synthetic work reported in 2011 and 2012. While focused on syntheses of inhibitors, some information on in vitro and in vivo testing of compounds is also included. Many of these reported compounds are reversible, competitive adenosine triphosphate (ATP) binding inhibitors, so given the structural similarities of many of these compounds to the adenine core, this review presents recent work on inhibitors based on where the synthetic chemistry was started, that is, inhibitor syntheses which started with purines/pyrimidines are followed by inhibitor syntheses which began with pyridines, pyrazines, azoles, and triazines then moves to inhibitors which bear no structural resemblance to adenine: liphagal, wortmannin and quercetin analogs. The review then finishes with a short section on recent syntheses of phosphotidyl inositol (PI) analogs since competitive PI binding inhibitors represent an alternative to the competitive ATP binding inhibitors which have received the most attention.
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Affiliation(s)
- Mark E Welker
- Department of Chemistry, Wake Forest University, PO Box 7486, Winston-Salem, NC 27109, USA.
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16
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Lin H. Isoform Selective PI3K-beta Inhibitors. CHINESE J CHEM 2013. [DOI: 10.1002/cjoc.201300030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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Discovery of phosphoinositide 3-kinases (PI3K) p110β isoform inhibitor 4-[2-hydroxyethyl(1-naphthylmethyl)amino]-6-[(2S)-2-methylmorpholin-4-yl]-1H-pyrimidin-2-one, an effective antithrombotic agent without associated bleeding and insulin resistance. Bioorg Med Chem Lett 2012; 22:6671-6. [DOI: 10.1016/j.bmcl.2012.08.102] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 08/25/2012] [Accepted: 08/27/2012] [Indexed: 12/13/2022]
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