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García-Raso A, Terrón A, López-Zafra A, García-Viada A, Barta A, Frontera A, Lorenzo J, Rodríguez-Calado S, Vázquez-López EM, Fiol JJ. Crystal structures of N6-modified-amino acid related nucleobase analogs (II): hybrid adenine-β-alanine and adenine-GABA molecules. NEW J CHEM 2019. [DOI: 10.1039/c9nj02279a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
H-Bonding networks and anion–π interactions in the crystal structures of N6-modified-amino acid adenine analogs are investigated using X-ray crystallography and DFT calculations.
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Affiliation(s)
- Angel García-Raso
- Departament de Química
- Universitat de les Illes Balears
- Crta. de Valldemossa km 7.5
- 07122 Palma (Baleares)
- Spain
| | - Angel Terrón
- Departament de Química
- Universitat de les Illes Balears
- Crta. de Valldemossa km 7.5
- 07122 Palma (Baleares)
- Spain
| | - Adela López-Zafra
- Departament de Química
- Universitat de les Illes Balears
- Crta. de Valldemossa km 7.5
- 07122 Palma (Baleares)
- Spain
| | | | - Agostina Barta
- Departament de Química
- Universitat de les Illes Balears
- Crta. de Valldemossa km 7.5
- 07122 Palma (Baleares)
- Spain
| | - Antonio Frontera
- Departament de Química
- Universitat de les Illes Balears
- Crta. de Valldemossa km 7.5
- 07122 Palma (Baleares)
- Spain
| | - Julia Lorenzo
- Instituto de Biotecnología y Biomedicina
- Departamento de Bioquímica y Biologia Molecular
- Universidad Autónoma de Barcelona
- Barcelona
- Spain
| | - Sergi Rodríguez-Calado
- Instituto de Biotecnología y Biomedicina
- Departamento de Bioquímica y Biologia Molecular
- Universidad Autónoma de Barcelona
- Barcelona
- Spain
| | - Ezequiel M. Vázquez-López
- Instituto de Investigación Sanitaria Galicia Sur/Universidade de Vigo
- Departamento de Química Inorgánica
- Facultade de Química
- Edificio Ciencias Experimentais
- E-36310 Vigo
| | - Juan J. Fiol
- Departament de Química
- Universitat de les Illes Balears
- Crta. de Valldemossa km 7.5
- 07122 Palma (Baleares)
- Spain
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2
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Yokoyama H, Sawada JI, Sato K, Ogo N, Kamei N, Ishikawa Y, Hara K, Asai A, Hashimoto H. Structural and Thermodynamic Basis of the Enhanced Interaction between Kinesin Spindle Protein Eg5 and STLC-type Inhibitors. ACS OMEGA 2018; 3:12284-12294. [PMID: 31459302 PMCID: PMC6644766 DOI: 10.1021/acsomega.8b00778] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 08/22/2018] [Indexed: 06/10/2023]
Abstract
For a better understanding of protein-inhibitor interactions, we report structural, thermodynamic, and biological analyses of the interactions between S-trityl-l-cysteine (STLC) derivatives and the motor domain of kinesin spindle protein Eg5. Binding of STLC-type inhibitors to Eg5 was enthalpically driven and entropically unfavorable. The introduction of a para-methoxy substituent in one phenyl ring of STLC enhances its inhibitory activity resulting from a larger enthalpy gain possibly due to the increased shape complementarity. The substituent fits to a recess in the binding pocket. To avoid steric hindrance, the substituted STLC is nudged toward the side opposite to the recess, which enhances the interaction of Eg5 with the remaining part of the inhibitor. Further introduction of an ethylene linkage between two phenyl rings enhances Eg5 inhibitory activity by reducing the loss of entropy in forming the complex. This study provides valuable examples of enhancing protein-inhibitor interactions without forming additional hydrogen bonds.
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Affiliation(s)
- Hideshi Yokoyama
- Faculty
of Pharmaceutical Sciences, Tokyo University
of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Jun-ichi Sawada
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Kohei Sato
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Naohisa Ogo
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Nanami Kamei
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Yoshinobu Ishikawa
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Kodai Hara
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Akira Asai
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hiroshi Hashimoto
- Department of Physical Biochemistry,
School of Pharmaceutical Sciences and Center for Drug
Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
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3
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Figueiredo P, Costa M, Pontes O, Baltazar F, Proença F. Adenine Derivatives: Promising Candidates for Breast Cancer Treatment. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800629] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Pedro Figueiredo
- Chemistry Department; University of Minho; Campus de Gualtar Braga Portugal
| | - Marta Costa
- Life and Health Sciences Research Institute (ICVS); University of Minho; Campus de Gualtar Braga Portugal
- ICVS/3B's - PT Government Associate Laboratory; Braga/Guimarães Portugal
| | - Olívia Pontes
- Life and Health Sciences Research Institute (ICVS); University of Minho; Campus de Gualtar Braga Portugal
- ICVS/3B's - PT Government Associate Laboratory; Braga/Guimarães Portugal
| | - Fátima Baltazar
- Life and Health Sciences Research Institute (ICVS); University of Minho; Campus de Gualtar Braga Portugal
- ICVS/3B's - PT Government Associate Laboratory; Braga/Guimarães Portugal
| | - Fernanda Proença
- Chemistry Department; University of Minho; Campus de Gualtar Braga Portugal
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4
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Liang C, Wu X, Li Z, Zhu J, Lu C, Shen Y. Design, synthesis and pharmacological evaluation of N-(5-chloro-2,4-dihydroxybenzoyl)-(R)-N-arylmethyl-1,2,3,4-tetrahydro-3-isoquinolinecarboxamides as potent Hsp90 inhibitors. Eur J Med Chem 2018; 143:85-96. [DOI: 10.1016/j.ejmech.2017.11.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/10/2017] [Accepted: 11/04/2017] [Indexed: 11/28/2022]
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5
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Li Y, Cao TT, Guo S, Zhong Q, Li CH, Li Y, Dong L, Zheng S, Wang G, Yin SF. Discovery of Novel Allopurinol Derivatives with Anticancer Activity and Attenuated Xanthine Oxidase Inhibition. Molecules 2016; 21:molecules21060771. [PMID: 27331805 PMCID: PMC5538589 DOI: 10.3390/molecules21060771] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/24/2016] [Accepted: 06/08/2016] [Indexed: 11/16/2022] Open
Abstract
A series of pyrazolo[3,4-d]pyrimidine derivatives related to allopurinol has been synthesized and evaluated for its cytotoxicity against a panel of three cancer cell lines as well as its xanthine oxidase (XOD) inhibitory activities. Among them, compound 4 showed potent cytotoxicity with IC50 values of 25.5 and 35.2 μM against human hepatoma carcinoma cell lines, BEL-7402 and SMMC-7221, respectively. The anticancer activity of 4 was comparable to that of Tanespimycin (17-N-allylamino-17-demethoxy geldanamycin, 17-AAG) that inhibited the growth of BEL-7402 and SMMC-7221 cells at IC50 values of 12.4 and 9.85 μM, respectively. However, unlike allopurinol, which is also a strong inhibitor of XOD, compound 4 is a much weaker XOD inhibitor, suggesting that the anticancer activities of the allopurinol derivatives may not be associated with XOD inhibition. Moreover, the cytotoxicity of 4 toward normal cells is significantly lower than that of 17-AAG, making 4 a promising lead compound for further optimization of structure-activity relationships that may lead to anticancer agents of clinical utility.
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Affiliation(s)
- Yong Li
- College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China.
| | - Ting-Ting Cao
- College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China.
| | - Shanchun Guo
- RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA 70125, USA.
| | - Qiu Zhong
- RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA 70125, USA.
| | - Cai-Hu Li
- College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China.
| | - Ying Li
- College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China.
| | - Lin Dong
- College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China.
| | - Shilong Zheng
- RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA 70125, USA.
| | - Guangdi Wang
- RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA 70125, USA.
| | - Shu-Fan Yin
- College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China.
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6
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Anighoro A, Stumpfe D, Heikamp K, Beebe K, Neckers LM, Bajorath J, Rastelli G. Computational polypharmacology analysis of the heat shock protein 90 interactome. J Chem Inf Model 2015; 55:676-86. [PMID: 25686391 DOI: 10.1021/ci5006959] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The design of a single drug molecule that is able to simultaneously and specifically interact with multiple biological targets is gaining major consideration in drug discovery. However, the rational design of drugs with a desired polypharmacology profile is still a challenging task, especially when these targets are distantly related or unrelated. In this work, we present a computational approach aimed at the identification of suitable target combinations for multitarget drug design within an ensemble of biologically relevant proteins. The target selection relies on the analysis of activity annotations present in molecular databases and on ligand-based virtual screening. A few target combinations were also inspected with structure-based methods to demonstrate that the identified dual-activity compounds are able to bind target combinations characterized by remote binding site similarities. Our approach was applied to the heat shock protein 90 (Hsp90) interactome, which contains several targets of key importance in cancer. Promising target combinations were identified, providing a basis for the computational design of compounds with dual activity. The approach may be used on any ensemble of proteins of interest for which known inhibitors are available.
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Affiliation(s)
- Andrew Anighoro
- †Life Sciences Department, University of Modena and Reggio Emilia, Via Campi 183, 41125 Modena, Italy
| | - Dagmar Stumpfe
- ‡Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
| | - Kathrin Heikamp
- ‡Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
| | - Kristin Beebe
- §Urological Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, United States
| | - Leonard M Neckers
- §Urological Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, United States
| | - Jürgen Bajorath
- ‡Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
| | - Giulio Rastelli
- †Life Sciences Department, University of Modena and Reggio Emilia, Via Campi 183, 41125 Modena, Italy
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7
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Papasergi MM, Patel BR, Tall GG. The G protein α chaperone Ric-8 as a potential therapeutic target. Mol Pharmacol 2014; 87:52-63. [PMID: 25319541 DOI: 10.1124/mol.114.094664] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Resistance to inhibitors of cholinesterase (Ric-8)A and Ric-8B are essential genes that encode positive regulators of heterotrimeric G protein α subunits. Controversy persists surrounding the precise way(s) that Ric-8 proteins affect G protein biology and signaling. Ric-8 proteins chaperone nucleotide-free Gα-subunit states during biosynthetic protein folding prior to G protein heterotrimer assembly. In organisms spanning the evolutionary window of Ric-8 expression, experimental perturbation of Ric-8 genes results in reduced functional abundances of G proteins because G protein α subunits are misfolded and degraded rapidly. Ric-8 proteins also act as Gα-subunit guanine nucleotide exchange factors (GEFs) in vitro. However, Ric-8 GEF activity could strictly be an in vitro phenomenon stemming from the ability of Ric-8 to induce partial Gα unfolding, thereby enhancing GDP release. Ric-8 GEF activity clearly differs from the GEF activity of G protein-coupled receptors (GPCRs). G protein βγ is inhibitory to Ric-8 action but obligate for receptors. It remains an open question whether Ric-8 has dual functions in cells and regulates G proteins as both a molecular chaperone and GEF. Clearly, Ric-8 has a profound influence on heterotrimeric G protein function. For this reason, we propose that Ric-8 proteins are as yet untested therapeutic targets in which pharmacological inhibition of the Ric-8/Gα protein-protein interface could serve to attenuate the effects of disease-causing G proteins (constitutively active mutants) and/or GPCR signaling. This minireview will chronicle the understanding of Ric-8 function, provide a comparative discussion of the Ric-8 molecular chaperoning and GEF activities, and support the case for why Ric-8 proteins should be considered potential targets for development of new therapies.
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Affiliation(s)
- Makaía M Papasergi
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, New York
| | - Bharti R Patel
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, New York
| | - Gregory G Tall
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, New York
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8
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Fragment-based hit discovery and structure-based optimization of aminotriazoloquinazolines as novel Hsp90 inhibitors. Bioorg Med Chem 2014; 22:4135-50. [PMID: 24980703 DOI: 10.1016/j.bmc.2014.05.056] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/21/2014] [Accepted: 05/23/2014] [Indexed: 12/26/2022]
Abstract
In the last decade the heat shock protein 90 (Hsp90) has emerged as a major therapeutic target and many efforts have been dedicated to the discovery of Hsp90 inhibitors as new potent anticancer agents. Here we report the identification of a novel class of Hsp90 inhibitors by means of a biophysical FAXS-NMR based screening of a library of fragments. The use of X-ray structure information combined with modeling studies enabled the fragment evolution of the initial triazoloquinazoline hit to a class of compounds with nanomolar potency and drug-like properties suited for further lead optimization.
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9
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Chiosis G, Kang Y, Sun W. Discovery and development of purine-scaffold Hsp90 inhibitors. Expert Opin Drug Discov 2013; 3:99-114. [PMID: 23480142 DOI: 10.1517/17460441.3.1.99] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The heat-shock protein 90 (Hsp90), an important target in cancer and other diseases, has become recently the focus of several drug discovery and development efforts. The initially identified natural-product inhibitors of Hsp90, such as geldanamycin, played a major role in elucidating its biological function and in determining its clinical relevance. Upcoming synthetic inhibitors, such as the purine-scaffold class, furthered our understanding on Hsp90 in cancer and neurodegenerative diseases and delivered what are promised to be clinical candidates with favorable pharmacologic profiles. This review intends to inform the reader on efforts ranging from the discovery of purine-scaffold Hsp90 inhibitors to their clinical translation as well as on their use as chemical tools to dissect the roles of Hsp90 in pathogenic systems.
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Affiliation(s)
- Gabriela Chiosis
- Memorial Sloan-Kettering Cancer Center, Department of Medicine and Program in Molecular Pharmacology and Chemistry, 1275 York Avenue, Box 482, New York, NY10021, USA +1 646 888 2235 ; +1 646 422 0416 ;
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10
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Literature Survey Part C: Heterocycle Synthesis. MICROWAVES IN ORGANIC AND MEDICINAL CHEMISTRY 2012. [DOI: 10.1002/9783527647828.ch7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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11
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Abstract
The protein tau is the most abundant microtubule associated protein in the central and peripheral nervous system. In the brain, tau plays a role in the assembly and stabilization of microtubules. The function of tau, however, appears to overlap with other microtubule binding proteins. The observation that tau is associated with neurodegenerative diseases has renewed interest in this protein. Various aspects of structure and biochemistry of tau, fibril formation and clinical perspectives, including therapeutic strategies are reviewed in this chapter.
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12
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Messaoudi S, Peyrat JF, Brion JD, Alami M. Heat-shock protein 90 inhibitors as antitumor agents: a survey of the literature from 2005 to 2010. Expert Opin Ther Pat 2011; 21:1501-42. [PMID: 21689065 DOI: 10.1517/13543776.2011.594041] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Heat-shock protein 90 (Hsp90) is a validated novel anticancer target with unique features. As a molecular chaperone, Hsp90 is implicated in maintaining the conformation, stability, activity and cellular localization of several key oncogenic client proteins that are involved in signal transduction pathways leading to proliferation, cell-cycle progression, apoptosis, angiogenesis and metastasis. As a result, inhibitors of Hsp90 achieve their promising anticancer activity through disruption of the Hsp90 protein function, thereby freezing the chaperone cycle; this in turn decreases the affinity of Hsp90 for client proteins, thus leading to proteasome-mediated degradation of oncogenic client proteins within cancer cells. AREAS COVERED This review provides recent background information on Hsp90 inhibitors. It also highlights a panel of compounds of interest reported in patents and discusses the clinical results of the promising drug candidates. EXPERT OPINION In the past 5 years, Hsp90 inhibitors have remained the focus of much interest as new potential anticancer agents. A large variety of scaffolds were studied in both academia and industry. Consequently, these significant research efforts have provided several promising drug candidates for further clinical development. Further progress in the development of Hsp90 inhibitors, combined with a deeper understanding of the chaperon characteristics, strengthens their promise in cancer therapy.
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Affiliation(s)
- Samir Messaoudi
- Univ Paris-Sud, CNRS, BioCIS-UMR 8076, Laboratoire de Chimie Thérapeutique, Faculté de Pharmacie, 5 rue J.-B. Clément, Châtenay-Malabry, F-92296, France
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13
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Roughley SD, Hubbard RE. How Well Can Fragments Explore Accessed Chemical Space? A Case Study from Heat Shock Protein 90. J Med Chem 2011; 54:3989-4005. [DOI: 10.1021/jm200350g] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | - Roderick E. Hubbard
- Vernalis (R&D) Ltd., Granta Park, Abington, Cambridge, CB21 6GB, U.K
- York Structural Biology Laboratory and Hull York Medical School, University of York, Heslington, York, YO10 5DD, U.K
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14
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Liu J, Wang F, Ma Z, Wang X, Wang Y. Structural determination of three different series of compounds as Hsp90 inhibitors using 3D-QSAR modeling, molecular docking and molecular dynamics methods. Int J Mol Sci 2011; 12:946-70. [PMID: 21541036 PMCID: PMC3083683 DOI: 10.3390/ijms12020946] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 01/11/2011] [Accepted: 01/25/2011] [Indexed: 01/23/2023] Open
Abstract
Hsp90 is involved in correcting, folding, maturation and activation of a diverse array of client proteins; it has also been implicated in the treatment of cancer in recent years. In this work, comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), molecular docking and molecular dynamics were performed on three different series of Hsp90 inhibitors to build 3D-QSAR models, which were based on the ligand-based or receptor-based methods. The optimum 3D-QSAR models exhibited reasonable statistical characteristics with averaging internal q2 > 0.60 and external r2pred > 0.66 for Benzamide tetrahydro-4H-carbazol-4-one analogs (BT), AT13387 derivatives (AT) and Dihydroxylphenyl amides (DA). The results revealed that steric effects contributed the most to the BT model, whereas H-bonding was more important to AT, and electrostatic, hydrophobic, H-bond donor almost contributed equally to the DA model. The docking analysis showed that Asp93, Tyr139 and Thr184 in Hsp90 are important for the three series of inhibitors. Molecular dynamics simulation (MD) further indicated that the conformation derived from docking is basically consistent with the average structure extracted from MD simulation. These results not only lead to a better understanding of interactions between these inhibitors and Hsp90 receptor but also provide useful information for the design of new inhibitors with a specific activity.
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Affiliation(s)
- Jianling Liu
- College of Life Sciences, Northwest University, Xi’an, Shaanxi 710069, China; E-Mails: (J.L.); (F.W.)
| | - Fangfang Wang
- College of Life Sciences, Northwest University, Xi’an, Shaanxi 710069, China; E-Mails: (J.L.); (F.W.)
| | - Zhi Ma
- Center of Bioinformatics, Northwest A&F University, Yangling, Shaanxi 712100, China; E-Mails: (Z.M.); (X.W.)
| | - Xia Wang
- Center of Bioinformatics, Northwest A&F University, Yangling, Shaanxi 712100, China; E-Mails: (Z.M.); (X.W.)
| | - Yonghua Wang
- Center of Bioinformatics, Northwest A&F University, Yangling, Shaanxi 712100, China; E-Mails: (Z.M.); (X.W.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-29-87092262; Fax: +86-29-87092262
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15
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Roughley S, Wright L, Brough P, Massey A, Hubbard RE. Hsp90 Inhibitors and Drugs from Fragment and Virtual Screening. Top Curr Chem (Cham) 2011; 317:61-82. [DOI: 10.1007/128_2011_181] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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16
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Saxena S, Chaudhaery SS, Varshney K, Saxena AK. Pharmacophore-based virtual screening and docking studies on Hsp90 inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2010; 21:445-462. [PMID: 20818581 DOI: 10.1080/1062936x.2010.501817] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Hsp90 (Heat shock protein 90) is an important therapeutic target for the treatment of cancer. To identify important chemical features for Hsp90 inhibitory activity, a 3D-QSAR pharmacophore model was developed using a set of 61 inhibitors (a training set of 31 and a test set of 30 compounds) belonging to a series of 2-amino-6-halopurine and 7'-substituted benzothiazolothio- and pyridinothiazolothio-purines. The best HypoGen model consisted of five pharmacophoric features: one hydrogen bond acceptor (HBA), one hydrogen bond donor (HBD) and three hydrophobic (HY) groups. It showed a high correlation coefficient (r = 0.943) and low root mean square deviation (RMSD = 0.751). This model was validated against 30 known Hsp90 inhibitors, where it showed a high predictive value for R(2)pred = 0.805], thus confirming that HY, HBA and HBD features are essential for Hsp90 inhibition. The validated pharmacophore model (Hypo-1) was used as a 3D query for virtual screening to retrieve potential inhibitors from the Maybridge and National Cancer Institute (NCI) databases. The hit compounds were subsequently subjected to molecular docking studies and, finally, five hits were prioritized as potential leads based on GoldScore function.
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Affiliation(s)
- S Saxena
- Medicinal and Process Chemistry Division, Central Drug Research Institute, Lucknow, India
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17
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Yi CH, Chen JZ, Shi SH, Hu GD, Zhang QG. A computational analysis of pyrazole-based inhibitors binding to Hsp90 using molecular dynamics simulation and the MM-GBSA method. MOLECULAR SIMULATION 2010. [DOI: 10.1080/08927021003628871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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18
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Taldone T, Chiosis G. Purine-scaffold Hsp90 inhibitors. Curr Top Med Chem 2010; 9:1436-46. [PMID: 19860732 DOI: 10.2174/156802609789895737] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Accepted: 09/07/2009] [Indexed: 01/05/2023]
Abstract
Hsp90 is a molecular chaperone with important roles in regulating the function of several proteins with potential pathogenic activity. Because many of these proteins are involved in cancer and neurodegenerative promoting pathways, Hsp90 has emerged as an attractive therapeutic target in these diseases. Molecules that bind to the N-terminal nucleotide pocket of Hsp90 inhibit its activity, and consequently, disrupt client protein function. A number of these inhibitors from several chemical classes are now known, and some are already in clinical trials. This review focuses on the purine class of Hsp90 inhibitors, their discovery through rational design, and on efforts aimed towards their optimization and development into clinically viable drugs for the treatment of cancer. Their potential towards neurodegenerative diseases will also be touched upon.
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Affiliation(s)
- Tony Taldone
- Program in Molecular Pharmacology and Chemistry and Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
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19
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Sgobba M, Rastelli G. Structure-Based and in silico Design of Hsp90 Inhibitors. ChemMedChem 2009; 4:1399-409. [DOI: 10.1002/cmdc.200900256] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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20
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The multiple roles of computational chemistry in fragment-based drug design. J Comput Aided Mol Des 2009; 23:459-73. [PMID: 19533374 DOI: 10.1007/s10822-009-9284-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 05/18/2009] [Indexed: 10/20/2022]
Abstract
Fragment-based drug discovery (FBDD) represents a change in strategy from the screening of molecules with higher molecular weights and physical properties more akin to fully drug-like compounds, to the screening of smaller, less complex molecules. This is because it has been recognised that fragment hit molecules can be efficiently grown and optimised into leads, particularly after the binding mode to the target protein has been first determined by 3D structural elucidation, e.g. by NMR or X-ray crystallography. Several studies have shown that medicinal chemistry optimisation of an already drug-like hit or lead compound can result in a final compound with too high molecular weight and lipophilicity. The evolution of a lower molecular weight fragment hit therefore represents an attractive alternative approach to optimisation as it allows better control of compound properties. Computational chemistry can play an important role both prior to a fragment screen, in producing a target focussed fragment library, and post-screening in the evolution of a drug-like molecule from a fragment hit, both with and without the available fragment-target co-complex structure. We will review many of the current developments in the area and illustrate with some recent examples from successful FBDD discovery projects that we have conducted.
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21
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Barker J, Barker O, Boggio R, Chauhan V, Cheng RK, Corden V, Courtney S, Edwards N, Falque V, Fusar F, Gardiner M, Hamelin EM, Hesterkamp T, Ichihara O, Jones R, Mather O, Mercurio C, Minucci S, Montalbetti CA, Müller A, Patel D, Phillips B, Varasi M, Whittaker M, Winkler D, Yarnold C. Fragment-based Identification of Hsp90 Inhibitors. ChemMedChem 2009; 4:963-6. [DOI: 10.1002/cmdc.200900011] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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5-Aryl-4-(5-substituted-2,4-dihydroxyphenyl)-1,2,3-thiadiazoles as inhibitors of Hsp90 chaperone. Bioorg Med Chem Lett 2009; 19:1089-92. [DOI: 10.1016/j.bmcl.2009.01.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Revised: 12/30/2008] [Accepted: 01/06/2009] [Indexed: 01/09/2023]
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23
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Tao H, Kang Y, Taldone T, Chiosis G. Microwave-assisted one step synthesis of 8-arylmethyl-9H-purin-6-amines. Bioorg Med Chem Lett 2009; 19:415-7. [PMID: 19058963 DOI: 10.1016/j.bmcl.2008.11.057] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Accepted: 11/17/2008] [Indexed: 10/21/2022]
Abstract
Molecular chaperone heat shock protein 90 (Hsp90) is an important target in cancer and neurodegenerative diseases, and has rapidly become the focus of several drug discovery efforts. Among small molecule Hsp90 inhibitors with clinical applicability are derivatives of 8-arylmethyl-9H-purin-6-amine class. Here we report the use of microwave-assisted chemistry for the successful one-pot delivery of 8-arylmethyl-9H-purin-6-amines. We discuss the applicability as well as the limitations of this method towards the creation of a large chemical diversity in the 8-arylmethyl-9H-purin-6-amine series.
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Affiliation(s)
- Hui Tao
- Program in Molecular Pharmacology and Chemistry and Department of Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 482, New York, NY 10021, USA
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24
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Singh S, Saxena AK. 2D-QSAR of purine-scaffold novel class of Hsp90 binders that inhibit the proliferation of cancer cells. Med Chem Res 2008. [DOI: 10.1007/s00044-007-9064-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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25
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Kasibhatla SR, Hong K, Biamonte MA, Busch DJ, Karjian PL, Sensintaffar JL, Kamal A, Lough RE, Brekken J, Lundgren K, Grecko R, Timony GA, Ran Y, Mansfield R, Fritz LC, Ulm E, Burrows FJ, Boehm MF. Rationally Designed High-Affinity 2-Amino-6-halopurine Heat Shock Protein 90 Inhibitors That Exhibit Potent Antitumor Activity. J Med Chem 2007; 50:2767-78. [PMID: 17488003 DOI: 10.1021/jm050752+] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heat shock protein 90 (Hsp90) is a molecular chaperone protein implicated in stabilizing the conformation and maintaining the function of many cell-signaling proteins. Many oncogenic proteins are more dependent on Hsp90 in maintaining their conformation, stability, and maturation than their normal counterparts. Furthermore, recent data show that Hsp90 exists in an activated form in malignant cells but in a latent inactive form in normal tissues, suggesting that inhibitors selective for the activated form could provide a high therapeutic index. Hence, Hsp90 is emerging as an exciting new target for the treatment of cancer. We now report on a novel series of 2-amino-6-halopurine Hsp90 inhibitors exemplified by 2-amino-6-chloro-9-(4-iodo-3,5-dimethylpyridin-2-ylmethyl)purine (30). These highly potent inhibitors (IC50 of 30 = 0.009 microM in a HER-2 degradation assay) also display excellent antiproliferative activity against various tumor cell lines (IC50 of 30 = 0.03 microM in MCF7 cells). Moreover, this class of inhibitors shows higher affinity for the activated form of Hsp90 compared to our earlier 8-sulfanylpurine Hsp90 inhibitor series. When administered orally to mice, these compounds exhibited potent tumor growth inhibition (>80%) in an N87 xenograft model, similar to that observed with 17-allylamino-17-desmethoxygeldanamycin (17-AAG), which is a compound currently in phase I/II clinical trials.
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Affiliation(s)
- Srinivas R Kasibhatla
- Department of Chemistry, Biogen Idec, Inc., 5200 Research Place, San Diego, CA 92122, USA.
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26
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Scoring functions and enrichment: a case study on Hsp90. BMC Bioinformatics 2007; 8:27. [PMID: 17257425 PMCID: PMC1790905 DOI: 10.1186/1471-2105-8-27] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 01/26/2007] [Indexed: 11/16/2022] Open
Abstract
Background The need for fast and accurate scoring functions has been driven by the increased use of in silico virtual screening twinned with high-throughput screening as a method to rapidly identify potential candidates in the early stages of drug development. We examine the ability of some the most common scoring functions (GOLD, ChemScore, DOCK, PMF, BLEEP and Consensus) to discriminate correctly and efficiently between active and non-active compounds among a library of ~3,600 diverse decoy compounds in a virtual screening experiment against heat shock protein 90 (Hsp90). Results Firstly, we investigated two ranking methodologies, GOLDrank and BestScorerank. GOLDrank is based on ranks generated using GOLD. The various scoring functions, GOLD, ChemScore, DOCK, PMF, BLEEP and Consensus, are applied to the pose ranked number one by GOLD for that ligand. BestScorerank uses multiple poses for each ligand and independently chooses the best ranked pose of the ligand according to each different scoring function. Secondly, we considered the effect of introducing the Thr184 hydrogen bond tether to guide the docking process towards a particular solution, and its effect on enrichment. Thirdly, we considered normalisation to account for the known bias of scoring functions to select larger molecules. All the scoring functions gave fairly similar enrichments, with the exception of PMF which was consistently the poorest performer. In most cases, GOLD was marginally the best performing individual function; the Consensus score usually performed similarly to the best single scoring function. Our best results were obtained using the Thr184 tether in combination with the BestScorerank protocol and normalisation for molecular weight. For that particular combination, DOCK was the best individual function; DOCK recovered 90% of the actives in the top 10% of the ranked list; Consensus similarly recovered 89% of the actives in its top 10%. Conclusion Overall, we demonstrate the validity of virtual screening as a method for identifying new leads from a pool of ligands with similar physicochemical properties and we believe that the outcome of this study provides useful insight into the setting up of a suitable docking and scoring protocol, resulting in enrichment of 'target active' compounds.
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27
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Blagg BSJ, Kerr TD. Hsp90 inhibitors: small molecules that transform the Hsp90 protein folding machinery into a catalyst for protein degradation. Med Res Rev 2006; 26:310-38. [PMID: 16385472 DOI: 10.1002/med.20052] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The 90 kDa heat shock proteins (Hsp90) are responsible for the conformational maturation of nascent polypeptides and the renaturation of denatured proteins. In transformed cells, numerous mutated and overexpressed proteins rely on the Hsp90 protein folding machinery for tumor progression. The Hsp90-mediated protein folding process is dependent upon ATP, and when inhibitors of ATP are present, the Hsp90 machinery is unable to fold client proteins into their biologically active form, which results in the degradation of protein substrates via the ubiquitin-proteasome pathway. Consequently, Hsp90 has evolved into a promising anti-cancer target because multiple oncogenic proteins can be simultaneously degraded as a consequence of Hsp90 inhibition. This review serves to explain the Hsp90 protein folding process, the impact of Hsp90 inhibition, the identification of natural product inhibitors, and the development of rationally designed inhibitors of the Hsp90 protein folding machinery.
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Affiliation(s)
- Brian S J Blagg
- The Department of Medicinal Chemistry, The University of Kansas, Lawrence, 66045, USA.
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28
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Zhang L, Fan J, Vu K, Hong K, Le Brazidec JY, Shi J, Biamonte M, Busch DJ, Lough RE, Grecko R, Ran Y, Sensintaffar JL, Kamal A, Lundgren K, Burrows FJ, Mansfield R, Timony GA, Ulm EH, Kasibhatla SR, Boehm MF. 7‘-Substituted Benzothiazolothio- and Pyridinothiazolothio-Purines as Potent Heat Shock Protein 90 Inhibitors. J Med Chem 2006; 49:5352-62. [PMID: 16913725 DOI: 10.1021/jm051146h] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report on the discovery of benzo- and pyridino- thiazolothiopurines as potent heat shock protein 90 inhibitors. The benzothiazole moiety is exceptionally sensitive to substitutions on the aromatic ring with a 7'-substituent essential for activity. Some of these compounds exhibit low nanomolar inhibition activity in a Her-2 degradation assay (28-150 nM), good aqueous solubility, and oral bioavailability profiles in mice. In vivo efficacy experiments demonstrate that compounds of this class inhibit tumor growth in an N87 human colon cancer xenograft model via oral administration as shown with compound 37 (8-(7-chlorobenzothiazol-2-ylsulfanyl)-9-(2-cyclopropylamino-ethyl)-9H- purin-6-ylamine).
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Affiliation(s)
- Lin Zhang
- Department of Medicinal Chemistry, Conforma Therapeutics Corporation, 9393 Towne Centre Drive, Suite 240, San Diego, California 92121, USA.
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29
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Sabat M, Vanrens JC, Clark MP, Brugel TA, Maier J, Bookland RG, Laufersweiler MJ, Laughlin SK, Golebiowski A, De B, Hsieh LC, Walter RL, Mekel MJ, Janusz MJ. The development of novel C-2, C-8, and N-9 trisubstituted purines as inhibitors of TNF-α production. Bioorg Med Chem Lett 2006; 16:4360-5. [PMID: 16750367 DOI: 10.1016/j.bmcl.2006.05.050] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Revised: 05/15/2006] [Accepted: 05/16/2006] [Indexed: 10/24/2022]
Abstract
A series of C-2, C-8, and N-9 trisubstituted purine based inhibitors of TNF-alpha production are described. The most potent analogs showed low nanomolar activity against LPS-induced TNF-alpha production in a THP-1 cell based assay. The SAR of the series was optimized with the aid of X-ray co-crystal structures of these inhibitors bound with mutated p38 (mp38).
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Affiliation(s)
- Mark Sabat
- Procter and Gamble Pharmaceuticals, Health Care Research Center, Mason, OH 45040, USA.
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30
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Georgakis GV, Younes A. Heat-shock protein 90 inhibitors in cancer therapy: 17AAG and beyond. Future Oncol 2006; 1:273-81. [PMID: 16555999 DOI: 10.1517/14796694.1.2.273] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Heat-shock protein 90 (HSP90) has diverse functions in mammalian cells. It acts as molecular chaperone, together with several co-chaperone molecules (such as Hop, Hip, p23, cdc37, Aha, and immunophilins). HSP90 binds to its client proteins (such as steroid receptors, AKT, Bcr-Abl, Apaf-1, survivin, cyclin dependent kinases which are involved in signal transduction that regulate cell cycle, survival, and death, and promote their proper protein folding, assembly, and transportation across different cellular compartments. Failure of Hsp90 chaperone activity leads to misfolding of client proteins, which leads to ubiquitination and proteasome degradation, and this deregulating cellular homeostasis. Since tumor cells frequently overexpress the active form of HSP90, which is more susceptible to inhibition by small molecules such as geldanamycin and its analogs, HSP90 became an attractive target for cancer therapy. This paper will review the recent advances in HSP90-biology and will discuss the emerging role of the HSP90 inhibitors such as 17-allylamino-17 demethoxy-geldanamycin and other HSP-90-directed small molecules in cancer therapy.
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Affiliation(s)
- Georgios V Georgakis
- The University of Texas, Department of Lymphoma and Myeloma, MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
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31
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Legraverend M, Grierson DS. The purines: potent and versatile small molecule inhibitors and modulators of key biological targets. Bioorg Med Chem 2006; 14:3987-4006. [PMID: 16503144 DOI: 10.1016/j.bmc.2005.12.060] [Citation(s) in RCA: 257] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Revised: 12/29/2005] [Accepted: 12/29/2005] [Indexed: 11/24/2022]
Abstract
The goal of this review is to highlight the wide range of biological activities displayed by purines, with particular emphasis on new purine-based agents which find potential application as chemical-biology tools and/or therapeutic agents. The expanding interest in the biological properties of polyfunctionalized purine derivatives issues, in large part, from the development of rapid high-throughput screening essays for new protein targets, and the corresponding development of efficient synthetic methodology adapted to the construction of highly diverse purine libraries. Purine-based compounds have found new applications as inducers of interferon and lineage-committed cell dedifferentiation, agonists and antagonists of adenosine receptors, ligands of corticotropin-releasing hormone receptors, and as inhibitors of HSP90, Src kinase, p38alpha MAP kinase, sulfotransferases, phosphodiesterases, and Cdks. The scope of application of purines in biology is most certainly far from being exhausted. Testing purine derivatives against the multitude of biological targets for which small molecule probes have not yet been found should thus be a natural reflex.
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Affiliation(s)
- Michel Legraverend
- UMR 176 CNRS-Institut Curie, Laboratoire de Pharmacochimie, Bât. 110, Centre Universitaire, 91405 Orsay, France.
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32
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Rodriquez M, Taddei M. Synthesis of Heterocycles via Microwave-Assisted Cycloadditions and Cyclocondensations. TOPICS IN HETEROCYCLIC CHEMISTRY 2006. [DOI: 10.1007/7081_005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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33
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Abstract
The molecular chaperone Hsp90 is a protein with important roles in maintaining the functional stability and viability of cells under a transforming pressure. Cancer cells harbour mutated oncogenic proteins or proteins with dysregulated function and the chaperone is required to maintain their folded and functionally active conformation. In addition, by chaperoning key proteins such as Raf-1, Akt, survivin and hTERT, Hsp90 regulates signalling pathways necessary for the growth, survival and limitless replicative potential of most tumours. Important elements of the apoptotic pathways are also regulated by Hsp90. Overall, these characteristics propose Hsp90 as an important target of whose inhibition may aim at a wide-range of oncogenic transformations. Several years into Hsp90 research have shed light into the feasibility, but also the limitations, of such an approach. In this review, the authors present the current understanding on the relevance and possibility of translating Hsp90 inhibitors into therapeutic agents in cancer therapy.
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Affiliation(s)
- Gabriela Chiosis
- Programme in Molecular Pharmacology and Chemistry, Department of Medicine, Memorial Sloan-Kettering Cancer Center, Box 482, New York, NY 10021, USA.
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34
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Howes R, Barril X, Dymock BW, Grant K, Northfield CJ, Robertson AGS, Surgenor A, Wayne J, Wright L, James K, Matthews T, Cheung KM, McDonald E, Workman P, Drysdale MJ. A fluorescence polarization assay for inhibitors of Hsp90. Anal Biochem 2006; 350:202-13. [PMID: 16460658 DOI: 10.1016/j.ab.2005.12.023] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2005] [Revised: 12/12/2005] [Accepted: 12/16/2005] [Indexed: 11/19/2022]
Abstract
Hsp90 encodes a ubiquitous molecular chaperone protein conserved among species which acts on multiple substrates, many of which are important cell-signaling proteins. Inhibition of Hsp90 function has been promoted as a mechanism to degrade client proteins involved in tumorigenesis and disease progression. Several assays to monitor inhibition of Hsp90 function currently exist but are limited in their use for a drug discovery campaign. Using data from the crystal structure of an initial hit compound, we have developed a fluorescence polarization assay to monitor binding of compounds to the ATP-binding site of Hsp90. This assay is very robust (Z' > 0.9) and can detect affinity of compounds with IC50s to 40 nM. We have used this assay in conjunction with cocrystal structures of small molecules to drive a structure-based design program aimed at the discovery and optimization of a novel class of potent Hsp90 inhibitors.
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Affiliation(s)
- R Howes
- Vernalis (Cambridge), Granta Park, Great Abington, Cambridge CB1 6GB, UK.
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35
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Biamonte MA, Shi J, Hong K, Hurst DC, Zhang L, Fan J, Busch DJ, Karjian PL, Maldonado AA, Sensintaffar JL, Yang YC, Kamal A, Lough RE, Lundgren K, Burrows FJ, Timony GA, Boehm MF, Kasibhatla SR. Orally Active Purine-Based Inhibitors of the Heat Shock Protein 90. J Med Chem 2005; 49:817-28. [PMID: 16420067 DOI: 10.1021/jm0503087] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Orally active Hsp90 inhibitors are of interest as potential chemotherapeutic agents. Recently, fully synthetic 8-benzyladenines and 8-sulfanyladenines such as 4 were disclosed as Hsp90 inhibitors, but these compounds are not water soluble and consequently have unacceptably low oral bioavailabilities. We now report that water-solubility can be achieved by inserting an amino functionality in the N(9) side chain. This results in compounds that are potent, soluble in aqueous media, and orally bioavailable. In an HER-2 degradation assay, the highest potency was achieved with the neopentylamine 42 (HER-2 IC(50) = 90 nM). In a murine tumor xenograft model (using the gastric cancer cell line N87), the H(3)PO(4) salts of the amines 38, 39, and 42 induced tumor growth inhibition when administered orally at 200 mg/kg/day. The amines 38, 39, and 42 are the first Hsp90 inhibitors shown to inhibit tumor growth upon oral dosage.
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Affiliation(s)
- Marco A Biamonte
- Department of Medicinal Chemistry, Conforma Therapeutics Corporation, San Diego, California 92121, USA.
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36
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He H, Zatorska D, Kim J, Aguirre J, Llauger L, She Y, Wu N, Immormino RM, Gewirth DT, Chiosis G. Identification of Potent Water Soluble Purine-Scaffold Inhibitors of the Heat Shock Protein 90. J Med Chem 2005; 49:381-90. [PMID: 16392823 DOI: 10.1021/jm0508078] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hsp90 is a chaperone protein that allows cancer cells to tolerate the many components of dysregulated pathways. Its inactivation may result in targeting multiple molecular alterations and, thus, in reverting the transformed phenotype. The PU-class, a purine-scaffold Hsp90 inhibitor series, has been reported to be potent and selective against Hsp90 both in vitro and in vivo models of cancer. Here, a series of this class was synthesized and evaluated as inhibitors of the chaperone. The structure-activity relationship and selectivity for tumor Hsp90 of compounds within the series is presented. The study identifies water soluble derivatives (>5 mM in PBS pH 7.4) of nanomolar potency (IC(50) approximately 50 nM) in cellular and animal models of cancer. Binding affinities of these compounds for Hsp90 correlate well with their biological activities. When administered in vivo to mice bearing MDA-MB-468 human breast cancer xenografted tumors, these agents result in pharmacologically relevant concentrations and, accordingly, in modulation of Hsp90-client proteins in tumors.
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Affiliation(s)
- Huazhong He
- Program in Molecular Pharmacology and Chemistry, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
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37
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Brough PA, Barril X, Beswick M, Dymock BW, Drysdale MJ, Wright L, Grant K, Massey A, Surgenor A, Workman P. 3-(5-Chloro-2,4-dihydroxyphenyl)-pyrazole-4-carboxamides as inhibitors of the Hsp90 molecular chaperone. Bioorg Med Chem Lett 2005; 15:5197-201. [PMID: 16213716 DOI: 10.1016/j.bmcl.2005.08.091] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2005] [Revised: 08/09/2005] [Accepted: 08/22/2005] [Indexed: 11/21/2022]
Abstract
Information from X-ray crystal structures of Hsp90 inhibitors bound to the human Hsp90 molecular chaperone was used to assist in the design of 3-(5-chloro-2,4-dihydroxyphenyl)-pyrazole-4-carboxamides as novel inhibitors of Hsp90. Accessing an extra interaction with the protein via Phe138 gave a significant increase in binding potency compared to similar analogues that do not make this interaction.
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Affiliation(s)
- Paul A Brough
- Vernalis Ltd, Granta Park, Great Abington, Cambridge CB1 6GB, UK.
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38
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Barril X, Brough P, Drysdale M, Hubbard RE, Massey A, Surgenor A, Wright L. Structure-based discovery of a new class of Hsp90 inhibitors. Bioorg Med Chem Lett 2005; 15:5187-91. [PMID: 16202589 DOI: 10.1016/j.bmcl.2005.08.092] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Revised: 08/11/2005] [Accepted: 08/22/2005] [Indexed: 12/01/2022]
Abstract
Docking-based virtual screening identified 1-(2-phenol)-2-naphthol compounds as a new class of Hsp90 inhibitors of low to sub-micromolar potency. Here we report the binding affinities and cellular activities of several members of this class. A high resolution crystal structure of the most potent compound reveals its binding mode in the ATP binding site of Hsp90, providing a rationale for the observed activity of the series and suggesting strategies for developing compounds with improved properties.
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Affiliation(s)
- Xavier Barril
- Vernalis (R&D) Ltd, Granta Park, Abington, Cambridge CB1 6GB, UK.
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39
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Abstract
Standing watch over the proteome, molecular chaperones are an ancient and evolutionarily conserved class of proteins that guide the normal folding, intracellular disposition and proteolytic turnover of many of the key regulators of cell growth, differentiation and survival. This essential guardian function is subverted during oncogenesis to allow malignant transformation and to facilitate rapid somatic evolution. Pharmacologically 'bribing' the essential guard duty of the chaperone HSP90 (heat-shock protein of 90 kDa) seems to offer a unique anticancer strategy of considerable promise.
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Affiliation(s)
- Luke Whitesell
- Steele Memorial Children's Research Center, University of Arizona, Tucson, Arizona 85724, USA.
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40
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Dymock BW, Barril X, Brough PA, Cansfield JE, Massey A, McDonald E, Hubbard RE, Surgenor A, Roughley SD, Webb P, Workman P, Wright L, Drysdale MJ. Novel, potent small-molecule inhibitors of the molecular chaperone Hsp90 discovered through structure-based design. J Med Chem 2005; 48:4212-5. [PMID: 15974572 DOI: 10.1021/jm050355z] [Citation(s) in RCA: 193] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The crystal structure of a previously reported screening hit 1 (CCT018159) bound to the N terminal domain of molecular chaperone Hsp90 has been used to design 5-amide analogues. These exhibit enhanced potency against the target in binding and functional assays with accompanying appropriate cellular pharmacodynamic changes. Compound 11 (VER-49009) compares favorably with the clinically evaluated 17-AAG.
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Affiliation(s)
- Brian W Dymock
- Vernalis Ltd., Granta Park, Great Abington, Cambridge, UK
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41
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Barril X, Morley SD. Unveiling the full potential of flexible receptor docking using multiple crystallographic structures. J Med Chem 2005; 48:4432-43. [PMID: 15974595 DOI: 10.1021/jm048972v] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the current challenges in docking studies is the inclusion of receptor flexibility. This is crucial because the binding sites of many therapeutic targets sample a wide range of conformational states, which has major consequences on molecular recognition. In this paper, we make use of very large sets of X-ray structures of cyclin dependent kinase 2 (CDK2) and heat shock protein 90 (HSP90) to assess the performance of flexible receptor docking in binding-mode prediction and virtual screening experiments. Flexible receptor docking performs much better than rigid receptor docking in the former application. Regarding the latter, we observe a significant improvement in the prediction of binding affinities, but owing to an increase in the number of false positives, this is not translated into better hit rates. A simple scoring scheme to correct this limitation is presented. More importantly, pitfalls inherent to flexible receptor docking have been identified and guidelines are presented to avoid them.
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Affiliation(s)
- Xavier Barril
- Vernalis (R&D), Granta Park, Abington, Cambridge CB1 6GB, UK.
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42
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Kreusch A, Han S, Brinker A, Zhou V, Choi HS, He Y, Lesley SA, Caldwell J, Gu XJ. Crystal structures of human HSP90alpha-complexed with dihydroxyphenylpyrazoles. Bioorg Med Chem Lett 2005; 15:1475-8. [PMID: 15713410 DOI: 10.1016/j.bmcl.2004.12.087] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2004] [Revised: 12/22/2004] [Accepted: 12/29/2004] [Indexed: 10/25/2022]
Abstract
A series of dihydroxyphenylpyrazole compounds were identified as a unique class of reversible Hsp90 inhibitors. The crystal structures for two of the identified compounds complexed with the N-terminal ATP binding domain of human Hsp90alpha were determined. The dihydroxyphenyl ring of the compounds fits deeply into the adenine binding pocket with the C2 hydroxyl group forming a direct hydrogen bond with the side chain of Asp93. The pyrazole ring forms hydrogen bonds to the backbone carbonyl of Gly97, the hydroxyl group of Thr184 and to a water molecule, which is present in all of the published HSP90 structures. One of the identified compounds (G3130) demonstrated cellular activities (in Her-2 degradation and activation of Hsp70 promoter) consistent with the inhibition of cellular Hsp90 functions.
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Affiliation(s)
- Andreas Kreusch
- Genomics Institute of the Novartis Research Foundation (GNF), 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
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43
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Cheung KMJ, Matthews TP, James K, Rowlands MG, Boxall KJ, Sharp SY, Maloney A, Roe SM, Prodromou C, Pearl LH, Aherne GW, McDonald E, Workman P. The identification, synthesis, protein crystal structure and in vitro biochemical evaluation of a new 3,4-diarylpyrazole class of Hsp90 inhibitors. Bioorg Med Chem Lett 2005; 15:3338-43. [PMID: 15955698 DOI: 10.1016/j.bmcl.2005.05.046] [Citation(s) in RCA: 176] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Revised: 05/10/2005] [Accepted: 05/11/2005] [Indexed: 01/21/2023]
Abstract
High-throughput screening identified the 3,4-diarylpyrazole CCT018159 as a novel and potent (7.1 microM) inhibitor of Hsp90 ATPase activity. Here, we describe the synthesis of CCT018159 and a number of close analogues together with data on their biochemical properties. Some initial structure-activity relationships are discussed, as well as the crystal structure of CCT018159 bound to Hsp90.
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Affiliation(s)
- Kwai-Ming J Cheung
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, Cancer Research UK and Haddow Laboratories, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
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44
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Liu J, Dang Q, Wei Z, Zhang H, Bai X. Parallel Solution-Phase Synthesis of a 2,6,8,9-Tetrasubstituted Purine Library via a Sulfur Intermediate. ACTA ACUST UNITED AC 2005; 7:627-36. [PMID: 16004508 DOI: 10.1021/cc049819p] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Purine analogues exhibiting a wide range of pharmacological activities have been considered a privileged structure in medicinal chemistry. In addition, the purine core consisting of four points of structural diversity is a well-sought scaffold in combinatorial chemistry. Although most of the efforts have been focused on 2,6,9-, 6,8,9-, or 2,8,9-trisubstituted purines, syntheses of 2,6,8,9-tetrasubstituted purines are rare. This paper presents a parallel solution phase approach for the synthesis of fully substituted purines via a 6-sulfur-substituted pyrimidine as the key intermediate. This strategy combining construction and modification of the purine ring thus increases the structural diversity of the final products. Sequential substitution of chlorines in 4,6-dichloro-2-methyl-5-nitropyrimidine with primary amine and benzylmercaptan afforded the 4-(substituted)amino-6-benzylthio-5-nitropyrimidine, which was readily converted to its diaminopyrimidine analogue by reduction of the nitro group. The diaminopyrimidine intermediate was cyclized to construct the purine ring with a C-8 substituent. Eventual oxidation of sulfur to sulfone and subsequent displacement by a primary or secondary amine provided the desired 2,6,8,9-tetrasubstituted purine analogues. This synthetic methodology was validated with the synthesis of a 216-member purine library.
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Affiliation(s)
- Jinglin Liu
- Center for Combinatorial Chemistry and Drug Discovery, Jilin University, 75 Jinlai Street, Changchun, Jilin 130012, China
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45
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Llauger L, He H, Kim J, Aguirre J, Rosen N, Peters U, Davies P, Chiosis G. Evaluation of 8-Arylsulfanyl, 8-Arylsulfoxyl, and 8-Arylsulfonyl Adenine Derivatives as Inhibitors of the Heat Shock Protein 90. J Med Chem 2005; 48:2892-905. [PMID: 15828828 DOI: 10.1021/jm049012b] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hsp90 is a chaperone protein with important roles in maintaining transformation and in elevating the survival and growth potential of cancer cells. Currently there is an increasing interest in developing inhibitors of this protein as anticancer therapeutics. One of such inhibitors, the purine-scaffold class, has been reported to be potent and selective against Hsp90 both in vitro and in vivo models of cancer. Here, a series of 8-arylsulfanyl, -sulfoxyl, and -sulfonyl adenine members of the purine class was synthesized and evaluated as inhibitors of the chaperone. The structure-activity relationship and selectivity for tumor Hsp90 of compounds within the series is presented. Our results suggest that 8-arylsulfanyl adenine derivatives are good inhibitors of chaperone activity, whereas oxidation of the sulfides to sulfoxides or sulfones leads to compounds of decreased activity. The study identifies derivative 11v as the most potent Hsp90 inhibitor of the purine-scaffold series published to date (EC(50) = 30 nM), and also as the compound of this class with highest selectivity for tumor vs normal cell Hsp90 (700 to 3000-fold). Most rewardingly, this work has allowed for the identification of Hsp90 inhibitors with selective affinities for Hsp90-client protein complexes, derivatives that may represent useful pharmacological tools in dissecting Hsp90-regulated processes.
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Affiliation(s)
- Laura Llauger
- Department of Medicine and Program in Molecular Pharmacology and Chemistry, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
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46
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Laufer SA, Domeyer DM, Scior TRF, Albrecht W, Hauser DRJ. Synthesis and biological testing of purine derivatives as potential ATP-competitive kinase inhibitors. J Med Chem 2005; 48:710-22. [PMID: 15689155 DOI: 10.1021/jm0408767] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
On the basis of ATP adenine, a series of adenine and purine derivatives was prepared and tested for their ability to inhibit a spectrum of disease-related kinases. There has been scant research investigating the potential of cosubstrate derived kinase inhibitors for other kinases than CDKs. Our inhibitor design combined the purine system from the original cosubstrate ATP and phenyl moieties in order to explore possible interactions with the different regions of the ATP binding site in several disease-related protein kinases. There have been a number of hits for the assayed substances, which led us to conclude that the spectrum of compounds may prove to be a valuable tool kit for the evaluation of bonding and selectivity patterns for a wide variety of kinases.
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Affiliation(s)
- Stefan A Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
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47
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Dymock BW, Drysdale MJ, McDonald E, Workman P. Inhibitors of HSP90 and other chaperones for the treatment of cancer. Expert Opin Ther Pat 2005. [DOI: 10.1517/13543776.14.6.837] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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48
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Wright L, Barril X, Dymock B, Sheridan L, Surgenor A, Beswick M, Drysdale M, Collier A, Massey A, Davies N, Fink A, Fromont C, Aherne W, Boxall K, Sharp S, Workman P, Hubbard RE. Structure-activity relationships in purine-based inhibitor binding to HSP90 isoforms. ACTA ACUST UNITED AC 2005; 11:775-85. [PMID: 15217611 DOI: 10.1016/j.chembiol.2004.03.033] [Citation(s) in RCA: 197] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2004] [Revised: 03/02/2004] [Accepted: 03/24/2004] [Indexed: 11/27/2022]
Abstract
Inhibition of the ATPase activity of the chaperone protein HSP90 is a potential strategy for treatment of cancers. We have determined structures of the HSP90alpha N-terminal domain complexed with the purine-based inhibitor, PU3, and analogs with enhanced potency both in enzyme and cell-based assays. The compounds induce upregulation of HSP70 and downregulation of the known HSP90 client proteins Raf-1, CDK4, and ErbB2, confirming that the molecules inhibit cell growth by a mechanism dependent on HSP90 inhibition. We have also determined the first structure of the N-terminal domain of HSP90beta, complexed with PU3. The structures allow a detailed rationale to be developed for the observed affinity of the PU3 class of compounds for HSP90 and also provide a structural framework for design of compounds with improved binding affinity and drug-like properties.
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Affiliation(s)
- Lisa Wright
- Vernalis (R&D) Ltd., Granta Park, Abington, Cambridge CB1 6GB, UK
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49
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Abstract
The molecular chaperone heat-shock protein 90 (Hsp90) is involved in the stabilization and conformational maturation of many signaling proteins that are deregulated in cancers. Hsp90 inhibition results in the proteasomal degradation of these client proteins and leads to potent antitumor activity. The Hsp90 inhibitor 17-allylaminogeldanamycin (17-AAG) is presently in clinical trials. Recent work has identified the role of Hsp90 in multiple signal transduction pathways and revealed that the molecular mechanism of tumor selectivity by Hsp90 inhibitors is the result of an activated, high-affinity conformation of Hsp90 in tumors. This review discusses these recent advances in the understanding of tumor Hsp90 for the treatment and diagnosis of cancer. In addition, the role of Hsp90 in non-oncological diseases will also be discussed.
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Affiliation(s)
- Adeela Kamal
- Department of Biology, Conforma Therapeutics Corporation, 9393 Towne Centre Drive, Suite 240, San Diego, CA 92121, USA.
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50
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Abstract
Rapidly evolving insights into the specific molecular genetic abnormalities that drive the growth and metastasis of breast cancer have led to the development of targeted therapeutics that do not rely on the generalized disruption of DNA metabolism and cell division for activity. Of particular interest are inhibitors of cellular signal transduction pathways involving tyrosine kinases as well as selective modulators of steroid hormone signaling, histone acetylation, angiogenesis and tumor cell apoptosis. Unique within this array of promising new agents, however, are compounds that target heat shock protein 90 (Hsp90). This molecular chaperone associates with a distinct, but surprisingly diverse, set of proteins that are referred to as Hsp90 client proteins. Hsp90 binds to these clients, and plays a key role in regulating their stability and function. Many of the proteins chaperoned by Hsp90 are involved in breast cancer progression and resistance to therapy, including the estrogen receptor, receptor tyrosine kinases of the erbB family, Akt, and mutant p53. Several small molecule inhibitors of Hsp90 have been identified that can deplete cellular levels of multiple oncogenic client proteins simultaneously by enhancing their ubiquitination and proteasome-mediated degradation. The activity of Hsp90 inhibitors has been well validated in preclinical breast cancer models, both in single-agent studies and in combination with conventional chemotherapy. One of these inhibitors, 17-allylamino, 17-demethoxygeldanamycin (17-AAG, NSC 330507) has recently completed phase I testing. The agent was well tolerated at drug exposures that were shown to cause modulation of Hsp90 client protein levels. Given the redundancy and complexity of the molecular abnormalities present in most breast cancers, the ability of Hsp90 inhibitors to alter the activity of multiple oncogenic targets may prove of unique therapeutic benefit.
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Affiliation(s)
- Jason Beliakoff
- Department of Urology, Stanford University School of Medicine, CA, USA
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