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Page N, Wappett M, O'Dowd CR, O'Rourke M, Gavory G, Zhang L, Rountree JSS, Jordan L, Barker O, Gibson H, Boyd C, Feutren-Burton S, McLean E, Trevitt G, Harrison T. Identification and development of a subtype-selective allosteric AKT inhibitor suitable for clinical development. Sci Rep 2022; 12:15715. [PMID: 36127435 PMCID: PMC9489722 DOI: 10.1038/s41598-022-20208-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 09/09/2022] [Indexed: 11/29/2022] Open
Abstract
The serine/threonine protein kinase AKT plays a pivotal role within the PI3K pathway in regulating cellular proliferation and apoptotic cellular functions, and AKT hyper-activation via gene amplification and/or mutation has been implicated in multiple human malignancies. There are 3 AKT isoenzymes (AKT1-3) which mediate critical, non-redundant functions. We present the discovery and development of ALM301, a novel, allosteric, sub-type selective inhibitor of AKT1/2. ALM301 binds in an allosteric pocket created by the combined movement of the PH domain and the catalytic domain, resulting in a DFG out conformation. ALM301 was shown to be highly selective against a panel of over 450 kinases and potently inhibited cellular proliferation. These effects were particularly pronounced in MCF-7 cells containing a PI3KCA mutation. Subsequent cellular downstream pathway analysis in this sensitive cell line revealed potent inhibition of pAKT signalling up to 48 h post dosing. ALM301 treatment was well tolerated in an MCF-7 xenograft model and led to a dose-dependent reduction in tumour growth. Enhanced efficacy was observed in combination with tamoxifen. In summary, ALM301 is a highly specific AKT 1/2 inhibitor with an excellent pharmacological profile suitable for further clinical development.
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Affiliation(s)
- Natalie Page
- Almac Discovery Ltd, Health Sciences Building, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Mark Wappett
- Almac Discovery Ltd, Health Sciences Building, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Colin R O'Dowd
- Almac Discovery Ltd, Health Sciences Building, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Martin O'Rourke
- Amphista Therapeutics, BioCity, Bo'Ness Rd, Newhouse, Chapelhall, Motherwell, ML1 5UH, UK
| | - Gerald Gavory
- Ridgeline Therapeutics GmbH, Technologiepark, Hochbergerstrasse 60C, 4057, Basel, Switzerland
| | - Lixin Zhang
- Shenyang University of Chemical Technology, Shenyang, China
| | - J S Shane Rountree
- Almac Discovery Ltd, Health Sciences Building, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Linda Jordan
- Globachem, Alderley Park, 2 BioHub, Mereside, Macclesfield, SK10 4TG, UK
| | - Oliver Barker
- Almac Discovery Ltd, Health Sciences Building, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Hayley Gibson
- Almac Discovery Ltd, Health Sciences Building, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Caroline Boyd
- Almac Discovery Ltd, Health Sciences Building, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Stephanie Feutren-Burton
- Almac Discovery Ltd, Health Sciences Building, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Estelle McLean
- Almac Discovery Ltd, Health Sciences Building, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Graham Trevitt
- Sygnature Discovery, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Timothy Harrison
- Almac Discovery Ltd, Health Sciences Building, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK. .,Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7AE, Northern Ireland, UK.
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Harrison T, Jacq X, O'Dowd C, Gavory G, Barker O, Bell C, Burkamp F, Burton S, Cassidy E, Helm M, Hewitt P, Page N, Rountree S, Rozycka E, Shepherd S, Whitehead S, Wappett M. Abstract LB-049: Targeting the ubiquitin-proteasome system by small molecule inhibition of the DUBome. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-lb-049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The current interest in protein homeostasis as a therapeutic strategy has highlighted the importance of protein ubiquitination as a post-translational modification. Protein degradation has been enabled by several approaches (e.g. small molecule degraders, molecular glues, and PROTACsTM). Deubiquitinating enzymes (DUBs) are proteases that catalyse the de-ubiquitination of protein substrates and as such offer an alternative way to regulate protein homeostasis. Furthermore, since ubiquitination also controls a plethora of regulatory functions beyond direct degradation, inhibition of DUBs provides additional opportunities to manipulate critical cellular processes. As a result of this dual role in protein degradation and signalling, as well as their increasing linkage to the etiology of numerous pathological conditions including cancer and neurodegeneration, DUBs have emerged as an attractive target class for the development of first-in-class medicines with high therapeutic impact. However until recently, DUBs have proven largely refractory to drug discovery efforts despite significant industry efforts. We have developed a purpose-built drug discovery platform (UbiPlex™) for the identification and development of DUB inhibitors. Herein, we will highlight significant recent developments to this platform including the addition of multiple DUB crystal structures (including fragments and small molecule co-crystals), biophysics, chemo/bio-informatics capabilities and focussed screening libraries. These developments have allowed the identification of novel, highly potent (e.g. IC50 < 100 nM), reversible inhibitors with drug like properties against multiple therapeutically relevant DUB targets. Selectivity profiles of representative inhibitors against panels of DUBs and other non-related enzymes (e.g. kinases, proteases) will be described, demonstrating that excellent selectivity is achievable. Finally, we will describe our progress towards the development of lead molecules with drug-like properties with the aim of rapidly establishing proof-of-concept studies in vivo for previously unexplored DUB targets. This work exemplifies the broad tractability and druggability of the DUBome and provides an alternative strategy for manipulation of the UPS. Furthermore, these potent, selective, cell penetrant molecules represent important chemical probes for pharmacological validation of the biological pathways associated with deubiquitinase inhibition as well as starting points for the development of new therapeutics for cancer and associated disorders.
Citation Format: Tim Harrison, Xavier Jacq, Colin O'Dowd, Gerald Gavory, Oliver Barker, Christina Bell, Frank Burkamp, Stephanie Burton, Eamon Cassidy, Matthew Helm, Peter Hewitt, Natalie Page, Shane Rountree, Ewelina Rozycka, Steven Shepherd, Steven Whitehead, Mark Wappett. Targeting the ubiquitin-proteasome system by small molecule inhibition of the DUBome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-049.
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Gavory G, O'Dowd C, Barker O, Bell C, Burkamp F, Burton S, Cassidy E, Costa J, Dossang A, Helm M, Henderson A, Hewitt P, Hughes C, McFarland M, Miel H, Page N, Proctor L, Rountree S, Rozycka E, Shepherd S, Treder A, Wappett M, Whitehead S, Harrison T. Abstract 1935: Accessing the cancer DUBome with UbiPlex: A bespoke drug discovery platform for deubiquitinase enzymes. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-1935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Over the past decade, protein ubiquitination has emerged as an important post-translational modification with regulatory functions in all important cellular processes. Deubiquitinating enzymes (DUBs) including ubiquitin specific proteases (USPs) are cysteine proteases that catalyse the de-ubiquitination of protein substrates.
As a result of their increasing implications in the etiology of numerous pathological conditions including cancer and immuno-oncology, DUBs have emerged as an attractive and promising target class for the development of first-in-class medicines with high therapeutic impact. However, despite 15 years of intense research DUBs have proven largely refractory to drug discovery efforts.
Herein, we further describe the application of UbiPlex™, our purpose-built drug discovery platform for the identification and development of DUB inhibitors. In particular, we will highlight the versatility and robustness of UbiPlex™ by reporting the outcome of our focussed library screening campaign on multiple DUBs in parallel and by describing the de novo hit ID, orthogonal validation and hit optimization activities on two USPs of relevance to cancer.
Multiple series of novel, highly potent (e.g. IC50 < 20 nM) and non-covalent inhibitors have been developed. Excellent selectivity profiles against a large panel of DUBs and other non-related enzymes (e.g. proteases) will be described. Further profiling indicated that these inhibitors are cell-permeable and exhibit potent target engagement in cells (e.g. EC50 < 30 nM). Finally, we will describe our progress towards the development of lead molecules with drug-like properties with the aim of rapidly establishing proof-of-concept studies in vivo.
In summary, this work further exemplifies the broad tractability and druggability of the DUBome and reports the discovery and profiling of novel highly potent and selective inhibitors beyond USP7. These molecules may provide opportunities for the development of new therapeutics for cancer and associated disorders.
Citation Format: Gerald Gavory, Colin O'Dowd, Oliver Barker, Christina Bell, Frank Burkamp, Stephanie Burton, Eamon Cassidy, Joana Costa, Anthony Dossang, Matt Helm, Ashling Henderson, Peter Hewitt, Caroline Hughes, Mary McFarland, Hugues Miel, Natalie Page, Lauren Proctor, Shane Rountree, Ewelina Rozycka, Steven Shepherd, Adam Treder, Mark Wappett, Steven Whitehead, Tim Harrison. Accessing the cancer DUBome with UbiPlex: A bespoke drug discovery platform for deubiquitinase enzymes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1935.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Matt Helm
- Almac Discovery, Belfast, United Kingdom
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Gavory G, O'Dowd C, Arkoudis E, Barker O, Cassidy E, Dossang A, Flasz J, Helm M, Hughes C, McClelland K, Miel H, Odrzywol E, Page N, Harrison T. Abstract 4869: Discovery and characterization of highly potent and selective USP7 inhibitors and benchmarking against clinical MDM2 antagonists. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Given the importance of USP7 in known oncogenic pathways and its emerging role in immuno-oncology, the identification of USP7 inhibitors has attracted considerable interest in the scientific community. However, despite substantial efforts over the past 15 years, the development of genuine deubiquitinase (DUB) inhibitors, which exhibit both drug-like properties and a well-defined mechanism of action, has proven particularly challenging.
In this study, we report the application of UbiPlexTM, our purpose-built DUB drug discovery platform, to USP7. In particular, we detail the identification, optimization and detailed characterization of a new class of non-covalent and highly potent USP7 inhibitors (IC50 < 10 nM). In addition, these inhibitors have shown exquisite selectivity for USP7 over other DUBs and proteases. We also disclose high-resolution co-crystal structures of USP7 in complex with these inhibitors that reveal an allosteric mode of binding.
Further profiling in cells demonstrated potent target engagement with endogenous USP7 (EC50 <20 nM). In line with the known biology of USP7, this effect induced the proteasomal degradation of MDM2, concomitant stabilization of p53 and induction of p21 in multiple cell lines. The identification and parallel profiling of inactive enantiomers further validated the on-target effect of our lead molecules. Finally, we report the identification of cell lines hyper-sensitive (EC50 < 30 nM) to USP7 inhibitors in both haematological and solid cancer cell line settings and demonstrate equal or superior activity when compared to clinically relevant MDM2 antagonists.
In summary, this work exemplifies the tractability and druggability of USP7 as a cancer target and provides new insights and directions for the potential clinical development of USP7 inhibitors.
Citation Format: Gerald Gavory, Colin O'Dowd, Elias Arkoudis, Oliver Barker, Eamon Cassidy, Anthony Dossang, Jakub Flasz, Matt Helm, Caroline Hughes, Keeva McClelland, Hugues Miel, Ewa Odrzywol, Natalie Page, Tim Harrison. Discovery and characterization of highly potent and selective USP7 inhibitors and benchmarking against clinical MDM2 antagonists [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4869.
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Affiliation(s)
| | | | | | | | | | | | | | - Matt Helm
- Almac Discovery, Belfast, United Kingdom
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O’Dowd CR, Helm MD, Rountree JSS, Flasz JT, Arkoudis E, Miel H, Hewitt PR, Jordan L, Barker O, Hughes C, Rozycka E, Cassidy E, McClelland K, Odrzywol E, Page N, Feutren-Burton S, Dvorkin S, Gavory G, Harrison T. Identification and Structure-Guided Development of Pyrimidinone Based USP7 Inhibitors. ACS Med Chem Lett 2018. [PMID: 29541367 DOI: 10.1021/acsmedchemlett.7b00512] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Ubiquitin specific protease 7 (USP7, HAUSP) has become an attractive target in drug discovery due to the role it plays in modulating Mdm2 levels and consequently p53. Increasing interest in USP7 is emerging due to its potential involvement in oncogenic pathways as well as possible roles in both metabolic and immune disorders in addition to viral infections. Potent, novel, and selective inhibitors of USP7 have been developed using both rational and structure-guided design enabled by high-resolution cocrystallography. Initial hits were identified via fragment-based screening, scaffold-hopping, and hybridization exercises. Two distinct subseries are described along with associated structure-activity relationship trends, as are initial efforts aimed at developing compounds suitable for in vivo experiments. Overall, these discoveries will enable further research into the wider biological role of USP7.
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Affiliation(s)
- Colin R. O’Dowd
- Almac Discovery Ltd., Centre for Precision Therapeutics, 97 Lisburn Road, Belfast, Northern Ireland BT9 7AE, United Kingdom
| | - Matthew D. Helm
- Almac Discovery Ltd., Centre for Precision Therapeutics, 97 Lisburn Road, Belfast, Northern Ireland BT9 7AE, United Kingdom
| | - J. S. Shane Rountree
- Almac Discovery Ltd., Centre for Precision Therapeutics, 97 Lisburn Road, Belfast, Northern Ireland BT9 7AE, United Kingdom
| | - Jakub T. Flasz
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Northern Ireland BT9 7AE, United Kingdom
| | - Elias Arkoudis
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Northern Ireland BT9 7AE, United Kingdom
| | - Hugues Miel
- Almac Discovery Ltd., Centre for Precision Therapeutics, 97 Lisburn Road, Belfast, Northern Ireland BT9 7AE, United Kingdom
| | - Peter R. Hewitt
- Almac Discovery Ltd., Centre for Precision Therapeutics, 97 Lisburn Road, Belfast, Northern Ireland BT9 7AE, United Kingdom
| | - Linda Jordan
- Almac Discovery Ltd., Centre for Precision Therapeutics, 97 Lisburn Road, Belfast, Northern Ireland BT9 7AE, United Kingdom
| | - Oliver Barker
- Almac Discovery Ltd., Centre for Precision Therapeutics, 97 Lisburn Road, Belfast, Northern Ireland BT9 7AE, United Kingdom
| | - Caroline Hughes
- Almac Discovery Ltd., Centre for Precision Therapeutics, 97 Lisburn Road, Belfast, Northern Ireland BT9 7AE, United Kingdom
| | - Ewelina Rozycka
- Almac Discovery Ltd., Centre for Precision Therapeutics, 97 Lisburn Road, Belfast, Northern Ireland BT9 7AE, United Kingdom
| | - Eamon Cassidy
- Almac Discovery Ltd., Centre for Precision Therapeutics, 97 Lisburn Road, Belfast, Northern Ireland BT9 7AE, United Kingdom
| | - Keeva McClelland
- Almac Discovery Ltd., Centre for Precision Therapeutics, 97 Lisburn Road, Belfast, Northern Ireland BT9 7AE, United Kingdom
| | - Ewa Odrzywol
- Almac Discovery Ltd., Centre for Precision Therapeutics, 97 Lisburn Road, Belfast, Northern Ireland BT9 7AE, United Kingdom
| | - Natalie Page
- Almac Discovery Ltd., Centre for Precision Therapeutics, 97 Lisburn Road, Belfast, Northern Ireland BT9 7AE, United Kingdom
| | - Stephanie Feutren-Burton
- Almac Discovery Ltd., Centre for Precision Therapeutics, 97 Lisburn Road, Belfast, Northern Ireland BT9 7AE, United Kingdom
| | - Scarlett Dvorkin
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Northern Ireland BT9 7AE, United Kingdom
| | - Gerald Gavory
- Almac Discovery Ltd., Centre for Precision Therapeutics, 97 Lisburn Road, Belfast, Northern Ireland BT9 7AE, United Kingdom
| | - Timothy Harrison
- Almac Discovery Ltd., Centre for Precision Therapeutics, 97 Lisburn Road, Belfast, Northern Ireland BT9 7AE, United Kingdom
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Northern Ireland BT9 7AE, United Kingdom
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Gavory G, O'Dowd CR, Helm MD, Flasz J, Arkoudis E, Dossang A, Hughes C, Cassidy E, McClelland K, Odrzywol E, Page N, Barker O, Miel H, Harrison T. Discovery and characterization of highly potent and selective allosteric USP7 inhibitors. Nat Chem Biol 2017; 14:118-125. [PMID: 29200206 DOI: 10.1038/nchembio.2528] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 10/18/2017] [Indexed: 12/26/2022]
Abstract
Given the importance of ubiquitin-specific protease 7 (USP7) in oncogenic pathways, identification of USP7 inhibitors has attracted considerable interest. Despite substantial efforts, however, the development of validated deubiquitinase (DUB) inhibitors that exhibit drug-like properties and a well-defined mechanism of action has proven particularly challenging. In this article, we describe the identification, optimization and detailed characterization of highly potent (IC50 < 10 nM), selective USP7 inhibitors together with their less active, enantiomeric counterparts. We also disclose, for the first time, co-crystal structures of a human DUB enzyme complexed with small-molecule inhibitors, which reveal a previously undisclosed allosteric binding site. Finally, we report the identification of cancer cell lines hypersensitive to USP7 inhibition (EC50 < 30 nM) and demonstrate equal or superior activity in these cell models compared to clinically relevant MDM2 antagonists. Overall, these findings demonstrate the tractability and druggability of DUBs, and provide important tools for additional target validation studies.
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Affiliation(s)
- Gerald Gavory
- Almac Discovery Ltd, Centre for Precision Therapeutics, Belfast, Northern Ireland, UK
| | - Colin R O'Dowd
- Almac Discovery Ltd, Centre for Precision Therapeutics, Belfast, Northern Ireland, UK
| | - Matthew D Helm
- Almac Discovery Ltd, Centre for Precision Therapeutics, Belfast, Northern Ireland, UK
| | - Jakub Flasz
- Centre for Cancer Research and Cell Biology, Queen's University, Belfast, Northern Ireland, UK
| | - Elias Arkoudis
- Centre for Cancer Research and Cell Biology, Queen's University, Belfast, Northern Ireland, UK
| | - Anthony Dossang
- Almac Discovery Ltd, Centre for Precision Therapeutics, Belfast, Northern Ireland, UK
| | - Caroline Hughes
- Almac Discovery Ltd, Centre for Precision Therapeutics, Belfast, Northern Ireland, UK
| | - Eamon Cassidy
- Almac Discovery Ltd, Centre for Precision Therapeutics, Belfast, Northern Ireland, UK
| | - Keeva McClelland
- Almac Discovery Ltd, Centre for Precision Therapeutics, Belfast, Northern Ireland, UK
| | - Ewa Odrzywol
- Almac Discovery Ltd, Centre for Precision Therapeutics, Belfast, Northern Ireland, UK
| | - Natalie Page
- Almac Discovery Ltd, Centre for Precision Therapeutics, Belfast, Northern Ireland, UK
| | - Oliver Barker
- Almac Discovery Ltd, Centre for Precision Therapeutics, Belfast, Northern Ireland, UK
| | - Hugues Miel
- Almac Discovery Ltd, Centre for Precision Therapeutics, Belfast, Northern Ireland, UK
| | - Timothy Harrison
- Almac Discovery Ltd, Centre for Precision Therapeutics, Belfast, Northern Ireland, UK.,Centre for Cancer Research and Cell Biology, Queen's University, Belfast, Northern Ireland, UK
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Gavory G, O'Dowd C, Rozycka E, Dossang A, Henderson A, Hughes C, Miel H, Barker O, Costa J, Hewitt P, McFarland M, Proctor L, Harrison T. Abstract 1181: Discovery and development of novel highly potent and selective inhibitors of USP19 using UbiPlex™. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Over the past decade, protein ubiquitination has emerged as an important post-translational modification with regulatory functions in all important cellular processes. Deubiquitinating enzymes (DUBs) including ubiquitin specific proteases (USPs) are cysteine proteases that catalyse the de-ubiquitination of protein substrates including tumor suppressors and oncogenes, hence regulating their levels and/or function. As a result of their increasing implications in the etiology of numerous pathological conditions including cancer, DUBs are emerging as an attractive and promising target class for the development of 1st in class medicines with high therapeutic impact. However, despite 15 years of intense research DUBs have proved largely refractory to drug discovery efforts.
Herein, we further describe the application of Ubi-Plex™, our drug discovery platform for the identification and optimisation of DUB inhibitors. In particular, we will highlight the versatility and robustness of Ubi-Plex™ by describing the outcome of our focussed library screening, hit identification, hit validation and elaboration activities on USP19.
A series of novel, highly potent (e.g. IC50 < 10 nM) and reversible USP19 inhibitors have been identified. Further profiling has also demonstrated excellent selectivity against a large panel of DUBs and other non-related enzymes (e.g. kinases, proteases). These inhibitors are cell-permeable and exhibit potent target engagement in cells with EC50 values < 30 nM. Finally, we will describe our progress towards the development of lead molecules with drug-like properties with the aim to rapidly establish in vivo proof-of-concept studies.
In summary, this work further exemplifies the tractability of the DUB target family and reports the discovery and detailed profiling of the first highly potent and selective inhibitors of USP19. These molecules may provide opportunities for the development of new anticancer therapeutics as well as for the treatment of muscle wasting disorders including cachexia.
Citation Format: Gerald Gavory, Colin O'Dowd, Ewelina Rozycka, Anthony Dossang, Ashling Henderson, Caroline Hughes, Hugues Miel, Oliver Barker, Joana Costa, Peter Hewitt, Mary McFarland, Lauren Proctor, Tim Harrison. Discovery and development of novel highly potent and selective inhibitors of USP19 using UbiPlex™ [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1181. doi:10.1158/1538-7445.AM2017-1181
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Langille BL, Perry R, Keefe D, Barker O, Marshall HD. Mitochondrial population structure and post-glacial dispersal of longnose sucker Catostomus catostomus in Labrador, Canada: evidence for multiple refugial origins and limited ongoing gene flow. J Fish Biol 2016; 89:1378-1392. [PMID: 27350593 DOI: 10.1111/jfb.13042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 04/27/2016] [Indexed: 06/06/2023]
Abstract
Two hundred and eighty-seven longnose sucker Catostomus catostomus were collected from 14 lakes in Labrador, 52 from three lakes in Ontario, 43 from two lakes in British Columbia and 32 from a lake in Yukon; a total of 414 in all. The resulting 34 haplotypes (20 in Labrador) contained moderate haplotypic diversity (h = 0·657) and relatively low nucleotide diversity (π = 3·730 × 10(-3) . Mean ϕST (0·453, P < 0·05) over all populations revealed distinct genetic structuring among C. catostomus populations across Canada, based on province, which was validated by the analysis and spatial analysis of molecular variance (c. 80% variation between provinces). These results probably reflect the historical imprint of recolonization from different refugia and possibly indicate limited ongoing gene flow within provinces. A haplotype network revealed one major and two minor clades within Labrador that were assigned to the Atlantic, Beringian and Mississippian refugia, respectively, with tests of neutrality and mismatch distribution indicative of a recent population expansion in Labrador, dated between c. 3500 and 8300 years ago.
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Affiliation(s)
- B L Langille
- Department of Biology, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, A1B 3X9, Canada
| | - R Perry
- Department of Environment and Conservation, Wildlife Division, Corner Brook, 117 Riverside Drive, P.O Box 2007, NL, A2H 7S1, Canada
| | - D Keefe
- Department of Environment and Conservation, Wildlife Division, Corner Brook, 117 Riverside Drive, P.O Box 2007, NL, A2H 7S1, Canada
| | - O Barker
- Department of Environment and Conservation, Wildlife Division, 10 Burns Road, Whitehorse, YK, Y1A 4Y9, Canada
| | - H D Marshall
- Department of Biology, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, A1B 3X9, Canada
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Gavory G, O'dowd C, McClelland K, Odrzywol E, Brown A, Burton S, Barker O, Burkamp F, Helm M, James I, Flasz J, Arkoudis E, Harrison T. Abstract LB-257: Discovery and characterization of novel, highly potent and selective USP7 inhibitors. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-lb-257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Over the past decade, protein ubiquitination has emerged as an important post-translational modification with roles in a plethora of cellular processes, and dysregulation in the ubiquitin proteasome system pathway (UPS) has been implicated in multiple human disorders including cancer.
Ubiquitin specific proteases (USPs) are cysteine proteases that catalyse the de-ubiquitination of numerous protein substrates including tumor suppressors and oncogenes, hence regulating their levels and/or functions. USPs therefore represent a fast growing and attractive target class for pharmacological intervention. USP7 in particular has attracted considerable attention for its implications in multiple key oncogenic pathways including most notably MDM2/p53, PTEN and DNA damage.
As part of a focussed effort towards targeting USPs, fragment screening was performed against a panel of family members, including USP7. Hits were identified by surface plasmon resonance and validated using orthogonal biophysical techniques (NMR, thermophoresis). Subsequent hit expansion identified molecules for which high-resolution co-crystal structures have been solved providing unique opportunities for structure-based design.
Medicinal chemistry optimisation has yielded a series of novel, reversible and potent USP7 inhibitors (e.g. IC50 < 10 nM) with excellent selectivity profiles against deubiquitinating (DUBs) and other non-related enzymes. These inhibitors are cell-permeable and also exhibit potent target engagement in cells (e.g. EC50 < 30 nM). In line with the mechanism of action, further cellular profiling has demonstrated effects on p53, p21 and MDM2 levels in a concentration-dependant manner. From a translational viewpoint, initial studies aimed at identifying cell lines sensitive to these inhibitors will also be discussed.
In summary, we report the discovery and detailed biochemical and cellular profiling of novel, potent and selective inhibitors of USP7. These molecules have drug-like properties and may provide opportunities for the development of new anticancer therapeutics.
Citation Format: Gerald Gavory, Colin O'dowd, Keeva McClelland, Ewa Odrzywol, Alan Brown, Stephanie Burton, Oliver Barker, Frank Burkamp, Matt Helm, Iain James, Jakub Flasz, Elias Arkoudis, Tim Harrison. Discovery and characterization of novel, highly potent and selective USP7 inhibitors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-257. doi:10.1158/1538-7445.AM2015-LB-257
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Affiliation(s)
| | | | | | | | - Alan Brown
- 1Almac Discovery, Craigavon, United Kingdom
| | | | | | | | - Matt Helm
- 1Almac Discovery, Craigavon, United Kingdom
| | - Iain James
- 1Almac Discovery, Craigavon, United Kingdom
| | - Jakub Flasz
- 2Queen's University Belfast, Belfast, United Kingdom
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Poulet B, de Souza R, Kent A, Saxon L, Barker O, Wilson A, Chang YM, Cake M, Pitsillides A. Intermittent applied mechanical loading induces subchondral bone thickening that may be intensified locally by contiguous articular cartilage lesions. Osteoarthritis Cartilage 2015; 23:940-8. [PMID: 25655679 PMCID: PMC4459965 DOI: 10.1016/j.joca.2015.01.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 01/19/2015] [Accepted: 01/23/2015] [Indexed: 02/02/2023]
Abstract
OBJECTIVES Changes in subchondral bone (SCB) and cross-talk with articular cartilage (AC) have been linked to osteoarthritis (OA). Using micro-computed tomography (micro-CT) this study: (1) examines changes in SCB architecture in a non-invasive loading mouse model in which focal AC lesions are induced selectively in the lateral femur, and (2) determines any modifications in the contralateral knee, linked to changes in gait, which might complicate use of this limb as an internal control. METHODS Right knee joints of CBA mice were loaded: once with 2 weeks of habitual use (n = 7), for 2 weeks (n = 8) or for 5 weeks (n = 5). Both left (contralateral) and right (loaded) knees were micro-CT scanned and the SCB and trabecular bone analysed. Gait analysis was also performed. RESULTS These analyses showed a significant increase in SCB thickness in the lateral compartments in joints loaded for 5 weeks, which was most marked in the lateral femur; the contralateral non-loaded knee also showed transient SCB thickening (loaded once and repetitively). Epiphyseal trabecular bone BV/TV and trabecular thickness were also increased in the lateral compartments after 5 weeks of loading, and in all joint compartments in the contralateral knee. Gait analysis showed that applied loading only affected gait in the contralateral himd-limb in all groups of mice from the second week after the first loading episode. CONCLUSIONS These data indicate a spatial link between SCB thickening and AC lesions following mechanical trauma, and the clear limitations associated with the use of contralateral joints as controls in such OA models, and perhaps in OA diagnosis.
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Affiliation(s)
- B. Poulet
- University College London, Royal Free Campus, London, UK
| | - R. de Souza
- Universidade Federal do Mato Grosso, Mato Grosso, Brazil
| | - A.V. Kent
- Royal Veterinary College, London, UK
| | - L. Saxon
- Royal Veterinary College, London, UK
| | - O. Barker
- Royal Veterinary College, London, UK
| | - A. Wilson
- Royal Veterinary College, London, UK
| | | | - M. Cake
- Murdoch University, Perth, Australia
| | - A.A. Pitsillides
- Royal Veterinary College, London, UK,Address correspondence and reprint requests to: A.A. Pitsillides, Comparative Biomedical Sciences, The Royal Veterinary College, Royal College Street, University of London, NW1 0TU, UK. Tel: 44-207-468-5245.
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11
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Jnoff E, Albrecht C, Barker JJ, Barker O, Beaumont E, Bromidge S, Brookfield F, Brooks M, Bubert C, Ceska T, Corden V, Dawson G, Duclos S, Fryatt T, Genicot C, Jigorel E, Kwong J, Maghames R, Mushi I, Pike R, Sands ZA, Smith MA, Stimson CC, Courade JP. Inside Cover: Binding Mode and Structure-Activity Relationships around Direct Inhibitors of the Nrf2-Keap1 Complex (ChemMedChem 4/2014). ChemMedChem 2014. [DOI: 10.1002/cmdc.201490011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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12
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Jnoff E, Albrecht C, Barker JJ, Barker O, Beaumont E, Bromidge S, Brookfield F, Brooks M, Bubert C, Ceska T, Corden V, Dawson G, Duclos S, Fryatt T, Genicot C, Jigorel E, Kwong J, Maghames R, Mushi I, Pike R, Sands ZA, Smith MA, Stimson CC, Courade JP. Binding Mode and Structure-Activity Relationships around Direct Inhibitors of the Nrf2-Keap1 Complex. ChemMedChem 2014; 9:699-705. [DOI: 10.1002/cmdc.201300525] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Indexed: 12/30/2022]
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13
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Heifetz A, Barker O, Morris GB, Law RJ, Slack M, Biggin PC. Combining Modelling and Site-Directed Mutagenesis to Explore Agonist Binding to Human Orexin Receptors. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Heifetz A, Barker O, Morris GB, Law R, Slack M, Biggin PC. Toward an understanding of agonist binding to human Orexin-1 and Orexin-2 receptors with G-protein-coupled receptor modeling and site-directed mutagenesis. Biochemistry 2013; 52:8246-60. [PMID: 24144388 PMCID: PMC3880013 DOI: 10.1021/bi401119m] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/21/2013] [Indexed: 02/06/2023]
Abstract
The class A G-protein-coupled receptors (GPCRs) Orexin-1 (OX1) and Orexin-2 (OX2) are located predominantly in the brain and are linked to a range of different physiological functions, including the control of feeding, energy metabolism, modulation of neuro-endocrine function, and regulation of the sleep-wake cycle. The natural agonists for OX1 and OX2 are two neuropeptides, Orexin-A and Orexin-B, which have activity at both receptors. Site-directed mutagenesis (SDM) has been reported on both the receptors and the peptides and has provided important insight into key features responsible for agonist activity. However, the structural interpretation of how these data are linked together is still lacking. In this work, we produced and used SDM data, homology modeling followed by MD simulation, and ensemble-flexible docking to generate binding poses of the Orexin peptides in the OX receptors to rationalize the SDM data. We also developed a protein pairwise similarity comparing method (ProS) and a GPCR-likeness assessment score (GLAS) to explore the structural data generated within a molecular dynamics simulation and to help distinguish between different GPCR substates. The results demonstrate how these newly developed methods of structural assessment for GPCRs can be used to provide a working model of neuropeptide-Orexin receptor interaction.
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Affiliation(s)
- Alexander Heifetz
- Evotec
(U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K.
| | - Oliver Barker
- Evotec
(U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K.
| | - G. Benjamin Morris
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Richard
J. Law
- Evotec
(U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K.
| | - Mark Slack
- Evotec
AG, Manfred Eigen Campus,
Essener Bogen 7, 22419 Hamburg, Germany
| | - Philip C. Biggin
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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15
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Heifetz A, Barker O, Verquin G, Wimmer N, Meutermans W, Pal S, Law RJ, Whittaker M. Fighting obesity with a sugar-based library: discovery of novel MCH-1R antagonists by a new computational-VAST approach for exploration of GPCR binding sites. J Chem Inf Model 2013; 53:1084-99. [PMID: 23590178 DOI: 10.1021/ci4000882] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Obesity is an increasingly common disease. While antagonism of the melanin-concentrating hormone-1 receptor (MCH-1R) has been widely reported as a promising therapeutic avenue for obesity treatment, no MCH-1R antagonists have reached the market. Discovery and optimization of new chemical matter targeting MCH-1R is hindered by reduced HTS success rates and a lack of structural information about the MCH-1R binding site. X-ray crystallography and NMR, the major experimental sources of structural information, are very slow processes for membrane proteins and are not currently feasible for every GPCR or GPCR-ligand complex. This situation significantly limits the ability of these methods to impact the drug discovery process for GPCR targets in "real-time", and hence, there is an urgent need for other practical and cost-efficient alternatives. We present here a conceptually pioneering approach that integrates GPCR modeling with design, synthesis, and screening of a diverse library of sugar-based compounds from the VAST technology (versatile assembly on stable templates) to provide structural insights on the MCH-1R binding site. This approach creates a cost-efficient new avenue for structure-based drug discovery (SBDD) against GPCR targets. In our work, a primary VAST hit was used to construct a high-quality MCH-1R model. Following model validation, a structure-based virtual screen yielded a 14% hit rate and 10 novel chemotypes of potent MCH-1R antagonists, including EOAI3367472 (IC50 = 131 nM) and EOAI3367474 (IC50 = 213 nM).
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Affiliation(s)
- Alexander Heifetz
- Evotec (UK), Ltd., Milton Park, Abingdon, Oxfordshire, United Kingdom.
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16
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Heifetz A, Morris GB, Biggin PC, Barker O, Fryatt T, Bentley J, Hallett D, Manikowski D, Pal S, Reifegerste R, Slack M, Law R. Study of Human Orexin-1 and -2 G-Protein-Coupled Receptors with Novel and Published Antagonists by Modeling, Molecular Dynamics Simulations, and Site-Directed Mutagenesis. Biochemistry 2012; 51:3178-97. [DOI: 10.1021/bi300136h] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Alexander Heifetz
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - G. Benjamin Morris
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Philip C. Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Oliver Barker
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Tara Fryatt
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Jonathan Bentley
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - David Hallett
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | | | - Sandeep Pal
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Rita Reifegerste
- Evotec AG, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | - Mark Slack
- Evotec AG, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | - Richard Law
- Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
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17
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Djung JF, Mears RJ, Montalbetti CA, Coulter TS, Golebiowski A, Carr AN, Barker O, Greis KD, Zhou S, Dolan E, Davis GF. The synthesis and evaluation of indolylureas as PKCα inhibitors. Bioorg Med Chem 2011; 19:2742-50. [DOI: 10.1016/j.bmc.2011.02.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Revised: 02/17/2011] [Accepted: 02/21/2011] [Indexed: 10/18/2022]
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18
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Barker JJ, Barker O, Courtney SM, Gardiner M, Hesterkamp T, Ichihara O, Mather O, Montalbetti CAGN, Müller A, Varasi M, Whittaker M, Yarnold CJ. Discovery of a Novel Hsp90 Inhibitor by Fragment Linking. ChemMedChem 2010; 5:1697-700. [DOI: 10.1002/cmdc.201000219] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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19
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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East SP, Bantry White C, Barker O, Barker S, Bennett J, Brown D, Andrew Boyd E, Brennan C, Chowdhury C, Collins I, Convers-Reignier E, Dymock BW, Fletcher R, Haydon DJ, Gardiner M, Hatcher S, Ingram P, Lancett P, Mortenson P, Papadopoulos K, Smee C, Thomaides-Brears HB, Tye H, Workman J, Czaplewski LG. Corrigendum to “DNA gyrase (GyrB)/topoisomerase IV (ParE) inhibitors: Synthesis and antibacterial activity” [Bioorg. Med. Chem. Lett. 19 (2009) 894]. Bioorg Med Chem Lett 2009. [DOI: 10.1016/j.bmcl.2008.11.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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21
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East SP, White CB, Barker O, Barker S, Bennett J, Brown D, Boyd EA, Brennan C, Chowdhury C, Collins I, Convers-Reignier E, Dymock BW, Fletcher R, Haydon DJ, Gardiner M, Hatcher S, Ingram P, Lancett P, Mortenson P, Papadopoulos K, Smee C, Thomaides-Brears HB, Tye H, Workman J, Czaplewski LG. DNA gyrase (GyrB)/topoisomerase IV (ParE) inhibitors: synthesis and antibacterial activity. Bioorg Med Chem Lett 2008; 19:894-9. [PMID: 19095445 DOI: 10.1016/j.bmcl.2008.11.102] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Revised: 11/24/2008] [Accepted: 11/26/2008] [Indexed: 10/21/2022]
Abstract
The synthesis and antibacterial activities of three chemotypes of DNA supercoiling inhibitors based on imidazolo[1,2-a]pyridine and [1,2,4]triazolo[1,5-a]pyridine scaffolds that target the ATPase subunits of DNA gyrase and topoisomerase IV (GyrB/ParE) is reported. The most potent scaffold was selected for optimization leading to a series with potent Gram-positive antibacterial activity and a low resistance frequency.
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Affiliation(s)
- Stephen P East
- Evotec (UK) Ltd, Discovery Services, 114 Milton Park, Abingdon, Oxfordshire OX14 4SA, UK
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