1
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Tamanini E, Miyamura S, Buck IM, Cons BD, Dawson L, East C, Futamura T, Goto S, Griffiths-Jones C, Hashimoto T, Heightman TD, Ishikawa S, Ito H, Kaneko Y, Kawato T, Kondo K, Kurihara N, McCarthy JM, Mori Y, Nagase T, Nakaishi Y, Reeks J, Sato A, Schöpf P, Tai K, Tamai T, Tisi D, Woolford AJA. Fragment-Based Discovery of a Novel, Brain Penetrant, Orally Active HDAC2 Inhibitor. ACS Med Chem Lett 2022; 13:1591-1597. [PMID: 36262388 PMCID: PMC9575179 DOI: 10.1021/acsmedchemlett.2c00272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/31/2022] [Indexed: 11/29/2022] Open
Abstract
Fragment-based ligand discovery was successfully applied to histone deacetylase HDAC2. In addition to the anticipated hydroxamic acid- and benzamide-based fragment screening hits, a low affinity (∼1 mM) α-amino-amide zinc binding fragment was identified, as well as fragments binding to other regions of the catalytic site. This alternative zinc-binding fragment was further optimized, guided by the structural information from protein-ligand complex X-ray structures, into a sub-μM, brain penetrant, HDAC2 inhibitor (17) capable of modulating histone acetylation levels in vivo.
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Affiliation(s)
- Emiliano Tamanini
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K.
| | - Shin Miyamura
- Otsuka
Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - Ildiko M. Buck
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K.
| | - Benjamin D. Cons
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K.
| | - Lee Dawson
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K.
| | - Charlotte East
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K.
| | - Takashi Futamura
- Otsuka
Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - Shintaro Goto
- Otsuka
Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | | | - Tetsuya Hashimoto
- Otsuka
Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - Tom D. Heightman
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K.
| | - Shunpei Ishikawa
- Otsuka
Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - Hideki Ito
- Otsuka
Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - Yosuke Kaneko
- Otsuka
Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - Tatsuya Kawato
- Otsuka
Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - Kazumi Kondo
- Otsuka
Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - Naoki Kurihara
- Otsuka
Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - James M. McCarthy
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K.
| | - Yukiko Mori
- Otsuka
Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - Tsuyoshi Nagase
- Otsuka
Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - Yuichiro Nakaishi
- Otsuka
Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - Judith Reeks
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K.
| | - Akimasa Sato
- Otsuka
Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - Patrick Schöpf
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K.
| | - Kuninori Tai
- Otsuka
Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - Taichi Tamai
- Otsuka
Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - Dominic Tisi
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K.
| | - Alison J.-A. Woolford
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K.
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2
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Norton D, Bonnette WG, Callahan JF, Carr MG, Griffiths-Jones CM, Heightman TD, Kerns JK, Nie H, Rich SJ, Richardson C, Rumsey W, Sanchez Y, Verdonk ML, Willems HMG, Wixted WE, Wolfe L, Woolford AJA, Wu Z, Davies TG. Fragment-Guided Discovery of Pyrazole Carboxylic Acid Inhibitors of the Kelch-like ECH-Associated Protein 1: Nuclear Factor Erythroid 2 Related Factor 2 (KEAP1:NRF2) Protein-Protein Interaction. J Med Chem 2021; 64:15949-15972. [PMID: 34705450 DOI: 10.1021/acs.jmedchem.1c01351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The NRF2-mediated cytoprotective response is central to cellular homoeostasis, and there is increasing interest in developing small-molecule activators of this pathway as therapeutics for diseases involving chronic oxidative stress. The protein KEAP1, which regulates NRF2, is a key point for pharmacological intervention, and we recently described the use of fragment-based drug discovery to develop a tool compound that directly disrupts the protein-protein interaction between NRF2 and KEAP1. We now present the identification of a second, chemically distinct series of KEAP1 inhibitors, which provided an alternative chemotype for lead optimization. Pharmacophoric information from our original fragment screen was used to identify new hit matter through database searching and to evolve this into a new lead with high target affinity and cell-based activity. We highlight how knowledge obtained from fragment-based approaches can be used to focus additional screening campaigns in order to de-risk projects through the rapid identification of novel chemical series.
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Affiliation(s)
- David Norton
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - William G Bonnette
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - James F Callahan
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Maria G Carr
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - Tom D Heightman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Jeffrey K Kerns
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Hong Nie
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Sharna J Rich
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - William Rumsey
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Yolanda Sanchez
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Marcel L Verdonk
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - William E Wixted
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Lawrence Wolfe
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | | | - Zining Wu
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Thomas G Davies
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
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3
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Johannes JW, Balazs A, Barratt D, Bista M, Chuba MD, Cosulich S, Critchlow SE, Degorce SL, Di Fruscia P, Edmondson SD, Embrey K, Fawell S, Ghosh A, Gill SJ, Gunnarsson A, Hande SM, Heightman TD, Hemsley P, Illuzzi G, Lane J, Larner C, Leo E, Liu L, Madin A, Martin S, McWilliams L, O'Connor MJ, Orme JP, Pachl F, Packer MJ, Pei X, Pike A, Schimpl M, She H, Staniszewska AD, Talbot V, Underwood E, Varnes JG, Xue L, Yao T, Zhang K, Zhang AX, Zheng X. Discovery of 5-{4-[(7-Ethyl-6-oxo-5,6-dihydro-1,5-naphthyridin-3-yl)methyl]piperazin-1-yl}- N-methylpyridine-2-carboxamide (AZD5305): A PARP1-DNA Trapper with High Selectivity for PARP1 over PARP2 and Other PARPs. J Med Chem 2021; 64:14498-14512. [PMID: 34570508 DOI: 10.1021/acs.jmedchem.1c01012] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Poly-ADP-ribose-polymerase (PARP) inhibitors have achieved regulatory approval in oncology for homologous recombination repair deficient tumors including BRCA mutation. However, some have failed in combination with first-line chemotherapies, usually due to overlapping hematological toxicities. Currently approved PARP inhibitors lack selectivity for PARP1 over PARP2 and some other 16 PARP family members, and we hypothesized that this could contribute to toxicity. Recent literature has demonstrated that PARP1 inhibition and PARP1-DNA trapping are key for driving efficacy in a BRCA mutant background. Herein, we describe the structure- and property-based design of 25 (AZD5305), a potent and selective PARP1 inhibitor and PARP1-DNA trapper with excellent in vivo efficacy in a BRCA mutant HBCx-17 PDX model. Compound 25 is highly selective for PARP1 over other PARP family members, with good secondary pharmacology and physicochemical properties and excellent pharmacokinetics in preclinical species, with reduced effects on human bone marrow progenitor cells in vitro.
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Affiliation(s)
- Jeffrey W Johannes
- Chemistry, Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Amber Balazs
- Chemistry, Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Derek Barratt
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 OWG, U.K
| | - Michal Bista
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 OWG, U.K
| | - Matthew D Chuba
- Chemistry, Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Sabina Cosulich
- Oncology Projects, Oncology R&D, AstraZeneca, Cambridge CB4 OWG, U.K
| | | | - Sébastien L Degorce
- Chemistry, Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | | | - Scott D Edmondson
- Chemistry, Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Kevin Embrey
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 OWG, U.K
| | - Stephen Fawell
- Oncology Discovery, Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Avipsa Ghosh
- Chemistry, Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Sonja J Gill
- Oncology Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB4 OWG, U.K
| | - Anders Gunnarsson
- Discovery Sciences, R&D Gothenburg, AstraZeneca, KJ2, Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Sudhir M Hande
- Chemistry, Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Tom D Heightman
- Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 OWG, U.K
| | - Paul Hemsley
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 OWG, U.K
| | | | - Jordan Lane
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 OWG, U.K
| | - Carrie Larner
- Oncology Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB4 OWG, U.K
| | - Elisabetta Leo
- Bioscience, Oncology R&D, AstraZeneca, Cambridge CB4 OWG, U.K
| | - Lina Liu
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Andrew Madin
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 OWG, U.K
| | - Scott Martin
- DMPK, Oncology R&D, AstraZeneca, Cambridge CB4 OWG, U.K
| | - Lisa McWilliams
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 OWG, U.K
| | - Mark J O'Connor
- Bioscience, Oncology R&D, AstraZeneca, Cambridge CB4 OWG, U.K
| | - Jonathan P Orme
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 OWG, U.K
| | - Fiona Pachl
- Discovery Sciences, R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Martin J Packer
- Computational Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 OWG, U.K
| | - Xiaohui Pei
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Andrew Pike
- DMPK, Oncology R&D, AstraZeneca, Cambridge CB4 OWG, U.K
| | | | - Hongyao She
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | | | - Verity Talbot
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 OWG, U.K
| | | | - Jeffrey G Varnes
- Chemistry, Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Lin Xue
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Tieguang Yao
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Ke Zhang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Andrew X Zhang
- Discovery Sciences, R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Xiaolan Zheng
- Chemistry, Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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4
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Heightman TD, Berdini V, Bevan L, Buck IM, Carr MG, Courtin A, Coyle JE, Day JEH, East C, Fazal L, Griffiths-Jones CM, Howard S, Kucia-Tran J, Martins V, Muench S, Munck JM, Norton D, O'Reilly M, Palmer N, Pathuri P, Peakman TM, Reader M, Rees DC, Rich SJ, Shah A, Wallis NG, Walton H, Wilsher NE, Woolford AJA, Cooke M, Cousin D, Onions S, Shannon J, Watts J, Murray CW. Discovery of ASTX029, A Clinical Candidate Which Modulates the Phosphorylation and Catalytic Activity of ERK1/2. J Med Chem 2021; 64:12286-12303. [PMID: 34387469 DOI: 10.1021/acs.jmedchem.1c00905] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aberrant activation of the mitogen-activated protein kinase pathway frequently drives tumor growth, and the ERK1/2 kinases are positioned at a key node in this pathway, making them important targets for therapeutic intervention. Recently, a number of ERK1/2 inhibitors have been advanced to investigational clinical trials in patients with activating mutations in B-Raf proto-oncogene or Ras. Here, we describe the discovery of the clinical candidate ASTX029 (15) through structure-guided optimization of our previously published isoindolinone lead (7). The medicinal chemistry campaign focused on addressing CYP3A4-mediated metabolism and maintaining favorable physicochemical properties. These efforts led to the identification of ASTX029, which showed the desired pharmacological profile combining ERK1/2 inhibition with suppression of phospho-ERK1/2 (pERK) levels, and in addition, it possesses suitable preclinical pharmacokinetic properties predictive of once daily dosing in humans. ASTX029 is currently in a phase I-II clinical trial in patients with advanced solid tumors.
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Affiliation(s)
- Tom D Heightman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Valerio Berdini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Luke Bevan
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Ildiko M Buck
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Maria G Carr
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Aurélie Courtin
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Joseph E Coyle
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - James E H Day
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Charlotte East
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Lynsey Fazal
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - Steven Howard
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Justyna Kucia-Tran
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Vanessa Martins
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Sandra Muench
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Joanne M Munck
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - David Norton
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Marc O'Reilly
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Nicholas Palmer
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Puja Pathuri
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Torren M Peakman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Michael Reader
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - David C Rees
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Sharna J Rich
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Alpesh Shah
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Nicola G Wallis
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Hugh Walton
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Nicola E Wilsher
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - Michael Cooke
- Sygnature Discovery Ltd., BioCity, Pennyfoot Street, Nottingham NG1 1GF, U.K
| | - David Cousin
- Sygnature Discovery Ltd., BioCity, Pennyfoot Street, Nottingham NG1 1GF, U.K
| | - Stuart Onions
- Sygnature Discovery Ltd., BioCity, Pennyfoot Street, Nottingham NG1 1GF, U.K
| | - Jonathan Shannon
- Sygnature Discovery Ltd., BioCity, Pennyfoot Street, Nottingham NG1 1GF, U.K
| | - John Watts
- Sygnature Discovery Ltd., BioCity, Pennyfoot Street, Nottingham NG1 1GF, U.K
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5
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Munck JM, Berdini V, Bevan L, Brothwood JL, Castro J, Courtin A, East C, Ferraldeschi R, Heightman TD, Hindley CJ, Kucia-Tran J, Lyons JF, Martins V, Muench S, Murray CW, Norton D, O'Reilly M, Reader M, Rees DC, Rich SJ, Richardson CJ, Shah AD, Stanczuk L, Thompson NT, Wilsher NE, Woolford AJA, Wallis NG. ASTX029, a Novel Dual-mechanism ERK Inhibitor, Modulates Both the Phosphorylation and Catalytic Activity of ERK. Mol Cancer Ther 2021; 20:1757-1768. [PMID: 34330842 DOI: 10.1158/1535-7163.mct-20-0909] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/11/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022]
Abstract
The MAPK signaling pathway is commonly upregulated in human cancers. As the primary downstream effector of the MAPK pathway, ERK is an attractive therapeutic target for the treatment of MAPK-activated cancers and for overcoming resistance to upstream inhibition. ASTX029 is a highly potent and selective dual-mechanism ERK inhibitor, discovered using fragment-based drug design. Because of its distinctive ERK-binding mode, ASTX029 inhibits both ERK catalytic activity and the phosphorylation of ERK itself by MEK, despite not directly inhibiting MEK activity. This dual mechanism was demonstrated in cell-free systems, as well as cell lines and xenograft tumor tissue, where the phosphorylation of both ERK and its substrate, ribosomal S6 kinase (RSK), were modulated on treatment with ASTX029. Markers of sensitivity were highlighted in a large cell panel, where ASTX029 preferentially inhibited the proliferation of MAPK-activated cell lines, including those with BRAF or RAS mutations. In vivo, significant antitumor activity was observed in MAPK-activated tumor xenograft models following oral treatment. ASTX029 also demonstrated activity in both in vitro and in vivo models of acquired resistance to MAPK pathway inhibitors. Overall, these findings highlight the therapeutic potential of a dual-mechanism ERK inhibitor such as ASTX029 for the treatment of MAPK-activated cancers, including those which have acquired resistance to inhibitors of upstream components of the MAPK pathway. ASTX029 is currently being evaluated in a first in human phase I-II clinical trial in patients with advanced solid tumors (NCT03520075).
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Affiliation(s)
| | | | - Luke Bevan
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | | | - Juan Castro
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | | | | | | | | | | | | | - John F Lyons
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | | | | | | | - David Norton
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | | | | | - David C Rees
- Astex Pharmaceuticals, Cambridge, United Kingdom
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6
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St Denis JD, Hall RJ, Murray CW, Heightman TD, Rees DC. Fragment-based drug discovery: opportunities for organic synthesis. RSC Med Chem 2020; 12:321-329. [PMID: 34041484 PMCID: PMC8130625 DOI: 10.1039/d0md00375a] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [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: 11/03/2020] [Accepted: 12/01/2020] [Indexed: 12/28/2022] Open
Abstract
This Review describes the increasing demand for organic synthesis to facilitate fragment-based drug discovery (FBDD), focusing on polar, unprotected fragments. In FBDD, X-ray crystal structures are used to design target molecules for synthesis with new groups added onto a fragment via specific growth vectors. This requires challenging synthesis which slows down drug discovery, and some fragments are not progressed into optimisation due to synthetic intractability. We have evaluated the output from Astex's fragment screenings for a number of programs, including urokinase-type plasminogen activator, hematopoietic prostaglandin D2 synthase, and hepatitis C virus NS3 protease-helicase, and identified fragments that were not elaborated due, in part, to a lack of commercially available analogues and/or suitable synthetic methodology. This represents an opportunity for the development of new synthetic research to enable rapid access to novel chemical space and fragment optimisation.
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Affiliation(s)
| | - Richard J Hall
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | | | - Tom D Heightman
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - David C Rees
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
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7
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Heightman TD, Callahan JF, Chiarparin E, Coyle JE, Griffiths-Jones C, Lakdawala AS, McMenamin R, Mortenson PN, Norton D, Peakman TM, Rich SJ, Richardson C, Rumsey WL, Sanchez Y, Saxty G, Willems HMG, Wolfe L, Woolford AJA, Wu Z, Yan H, Kerns JK, Davies TG. Structure–Activity and Structure–Conformation Relationships of Aryl Propionic Acid Inhibitors of the Kelch-like ECH-Associated Protein 1/Nuclear Factor Erythroid 2-Related Factor 2 (KEAP1/NRF2) Protein–Protein Interaction. J Med Chem 2019; 62:4683-4702. [DOI: 10.1021/acs.jmedchem.9b00279] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Tom D. Heightman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - James F. Callahan
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | | | - Joseph E. Coyle
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - Ami S. Lakdawala
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Rachel McMenamin
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Paul N. Mortenson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - David Norton
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Torren M. Peakman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Sharna J. Rich
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - William L. Rumsey
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Yolanda Sanchez
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Gordon Saxty
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - Lawrence Wolfe
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | | | - Zining Wu
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Hongxing Yan
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Jeffrey K. Kerns
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Thomas G. Davies
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
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8
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Grainger R, Heightman TD, Ley SV, Lima F, Johnson CN. Enabling synthesis in fragment-based drug discovery by reactivity mapping: photoredox-mediated cross-dehydrogenative heteroarylation of cyclic amines. Chem Sci 2019; 10:2264-2271. [PMID: 30881651 PMCID: PMC6385880 DOI: 10.1039/c8sc04789h] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [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: 10/26/2018] [Accepted: 12/19/2018] [Indexed: 12/22/2022] Open
Abstract
In fragment-based drug discovery (FBDD), a weakly binding fragment hit is elaborated into a potent ligand by bespoke functionalization along specific directions (growth vectors) from the fragment core in order to complement the 3D structure of the target protein. This structure-based design approach can present significant synthetic challenges, as growth vectors often originate on sp2 or sp3 ring carbons which are not the most synthetically accessible points on the fragment. To address this issue and expedite synthesis in FBDD, we established a nanogram-to-gram workflow for the development of enabling synthetic transformations, such as the direct C-H functionalization of heterocycles. This novel approach deploys high-throughput experimentation (HTE) in 1536-well microtiter plates (MTPs) facilitated by liquid handling robots to screen reaction conditions on the nanomolar scale; subsequently the reaction is upscaled in a continuous flow to generate gram-quantities of the material. In this paper, we disclose the use of this powerful workflow for the development of a photoredox-mediated cross-dehydrogenative coupling of fragments and medicinally relevant heterocyclic precursors via Minisci-type addition of α-amino radicals to electron-deficient heteroarenes. The optimized reaction conditions were employed on the milligram-scale on a diverse set of 112 substrates to map out structure-reactivity relationships (SRRs) of the transformation. The coupling exhibits excellent tolerance to a variety of functional groups and N-rich heteroarenes relevant to FBDD and was upscaled in a continuous flow to afford gram-quantities of pharmaceutically relevant sp2-sp3 privileged architectures.
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Affiliation(s)
- Rachel Grainger
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge , CB4 0QA , UK . ;
| | - Tom D Heightman
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge , CB4 0QA , UK . ;
| | - Steven V Ley
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
| | - Fabio Lima
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
- Novartis Pharma AG , Novartis Campus , 4002 Basel , Switzerland
| | - Christopher N Johnson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge , CB4 0QA , UK . ;
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9
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Lebraud H, Surova O, Courtin A, O'Reilly M, Valenzano CR, Nordlund P, Heightman TD. Quantitation of ERK1/2 inhibitor cellular target occupancies with a reversible slow off-rate probe. Chem Sci 2018; 9:8608-8618. [PMID: 30568786 PMCID: PMC6253716 DOI: 10.1039/c8sc02754d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 06/22/2018] [Accepted: 09/15/2018] [Indexed: 11/21/2022] Open
Abstract
Target engagement is a key concept in drug discovery and its direct measurement can provide a quantitative understanding of drug efficacy and/or toxicity. Failure to demonstrate target occupancy in relevant cells and tissues has been recognised as a contributing factor to the low success rate of clinical drug development. Several techniques are emerging to quantify target engagement in cells; however, in situ measurements remain challenging, mainly due to technical limitations. Here, we report the development of a non-covalent clickable probe, based on SCH772984, a slow off-rate ERK1/2 inhibitor, which enabled efficient pull down of ERK1/2 protein via click reaction with tetrazine tagged agarose beads. This was used in a competition setting to measure relative target occupancy by selected ERK1/2 inhibitors. As a reference we used the cellular thermal shift assay, a label-free biophysical assay relying solely on ligand-induced thermodynamic stabilization of proteins. To validate the EC50 values measured by both methods, the results were compared with IC50 data for the phosphorylation of RSK, a downstream substrate of ERK1/2 used as a functional biomarker of ERK1/2 inhibition. We showed that a slow off-rate reversible probe can be used to efficiently pull down cellular proteins, significantly extending the potential of the approach beyond the need for covalent or photoaffinity warheads.
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Affiliation(s)
- Honorine Lebraud
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . ;
| | - Olga Surova
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . ;
- Department of Oncology-Pathology , Karolinska Institute , CCK R8:01 , Karolinska Hospital , 171 76 Stockholm , Sweden
| | - Aurélie Courtin
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . ;
| | - Marc O'Reilly
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . ;
| | - Chiara R Valenzano
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . ;
| | - Pär Nordlund
- Department of Oncology-Pathology , Karolinska Institute , CCK R8:01 , Karolinska Hospital , 171 76 Stockholm , Sweden
| | - Tom D Heightman
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . ;
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10
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Lebraud H, Noble RA, Phillips N, Heam K, Castro J, Zhao Y, Newell DR, Lunec J, Wedge SR, Heightman TD. Highly Potent Clickable Probe for Cellular Imaging of MDM2 and Assessing Dynamic Responses to MDM2-p53 Inhibition. Bioconjug Chem 2018; 29:2100-2106. [PMID: 29851469 DOI: 10.1021/acs.bioconjchem.8b00315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
MDM2 is a key negative regulator of the p53 tumor suppressor. Direct binding of MDM2 to p53 represses the protein's transcriptional activity and induces its polyubiquitination, targeting it for degradation by the proteasome. Consequently, small molecule inhibitors that antagonize MDM2-p53 binding, such as RG7388, have progressed into clinical development aiming to reactivate p53 function in TP53 wild-type tumors. Here, we describe the design, synthesis, and biological evaluation of a trans-cyclooctene tagged derivative of RG7388, RG7388-TCO, which showed high cellular potency and specificity for MDM2. The in-cell reaction of RG7388-TCO with a tetrazine-tagged BODIPY dye enabled fluorescence imaging of endogenous MDM2 in SJSA-1 and T778 tumor cells. RG7388-TCO was also used to pull down MDM2 by reaction with tetrazine-tagged agarose beads in SJSA-1 lysates. The data presented show that RG733-TCO enables precise imaging of MDM2 in cells and can permit a relative assessment of target engagement and MDM2-p53 antagonism in vitro.
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Affiliation(s)
- Honorine Lebraud
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge CB4 0QA , United Kingdom
| | - Richard A Noble
- Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School , Newcastle University , Framlington Place , Newcastle-upon-Tyne NE2 4HH , United Kingdom
| | - Nicole Phillips
- Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School , Newcastle University , Framlington Place , Newcastle-upon-Tyne NE2 4HH , United Kingdom
| | - Keisha Heam
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge CB4 0QA , United Kingdom
| | - Juan Castro
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge CB4 0QA , United Kingdom
| | - Yan Zhao
- Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School , Newcastle University , Framlington Place , Newcastle-upon-Tyne NE2 4HH , United Kingdom
| | - David R Newell
- Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School , Newcastle University , Framlington Place , Newcastle-upon-Tyne NE2 4HH , United Kingdom
| | - John Lunec
- Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School , Newcastle University , Framlington Place , Newcastle-upon-Tyne NE2 4HH , United Kingdom
| | - Stephen R Wedge
- Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School , Newcastle University , Framlington Place , Newcastle-upon-Tyne NE2 4HH , United Kingdom
| | - Tom D Heightman
- Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge CB4 0QA , United Kingdom
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11
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Heightman TD, Berdini V, Braithwaite H, Buck IM, Cassidy M, Castro J, Courtin A, Day JEH, East C, Fazal L, Graham B, Griffiths-Jones CM, Lyons JF, Martins V, Muench S, Munck JM, Norton D, O’Reilly M, Palmer N, Pathuri P, Reader M, Rees DC, Rich SJ, Richardson C, Saini H, Thompson NT, Wallis NG, Walton H, Wilsher NE, Woolford AJA, Cooke M, Cousin D, Onions S, Shannon J, Watts J, Murray CW. Fragment-Based Discovery of a Potent, Orally Bioavailable Inhibitor That Modulates the Phosphorylation and Catalytic Activity of ERK1/2. J Med Chem 2018; 61:4978-4992. [DOI: 10.1021/acs.jmedchem.8b00421] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Tom D. Heightman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Valerio Berdini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Hannah Braithwaite
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Ildiko M. Buck
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Megan Cassidy
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Juan Castro
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Aurélie Courtin
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - James E. H. Day
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Charlotte East
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Lynsey Fazal
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Brent Graham
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | | | - John F. Lyons
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Vanessa Martins
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Sandra Muench
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Joanne M. Munck
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - David Norton
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Marc O’Reilly
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Nick Palmer
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Puja Pathuri
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Michael Reader
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - David C. Rees
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Sharna J. Rich
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | | | - Harpreet Saini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Neil T. Thompson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Nicola G. Wallis
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Hugh Walton
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | - Nicola E. Wilsher
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, U.K
| | | | - Michael Cooke
- Sygnature Discovery Ltd., BioCity, Pennyfoot Street, Nottingham, NG1 1GF, U.K
| | - David Cousin
- Sygnature Discovery Ltd., BioCity, Pennyfoot Street, Nottingham, NG1 1GF, U.K
| | - Stuart Onions
- Sygnature Discovery Ltd., BioCity, Pennyfoot Street, Nottingham, NG1 1GF, U.K
| | - Jonathan Shannon
- Sygnature Discovery Ltd., BioCity, Pennyfoot Street, Nottingham, NG1 1GF, U.K
| | - John Watts
- Sygnature Discovery Ltd., BioCity, Pennyfoot Street, Nottingham, NG1 1GF, U.K
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12
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Heightman TD, Berdini V, Braithwaite H, Buck I, Cassidy M, Castro J, Courtin A, Day J, East C, Fazal L, Graham B, Griffiths-Jones C, Lyons J, Martins V, Muench S, Munck J, Norton D, O'Reilly M, Palmer N, Pathuri P, Reader M, Rees D, Rich S, Richardson C, Saini H, Thompson N, Wallis N, Walton H, Wilsher N, Woolford A, Murray C. Abstract B161: Fragment-based discovery of a highly potent, orally bioavailable ERK1/2 inhibitor that modulates the phosphorylation and catalytic activity of ERK1/2. Mol Cancer Ther 2018. [DOI: 10.1158/1535-7163.targ-17-b161] [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 RAS-RAF-MEK-ERK signalling cascade is activated through mutations in RAS or RAF in over 30% of cancers. The successful development of inhibitors of BRAF and MEK kinases has led to effective treatment particularly of melanomas whose tumor growth is driven by activating mutations in BRAF such as V600E. Despite these successes, resistance emerges after several months, leading to increased signaling through ERK1/2. This has prompted the development of direct inhibitors of ERK1/2, several of which are in early clinical trials. The majority of clinical ERK1/2 inhibitors are ATP competitive, blocking ERK1/2 catalytic phosphorylation of downstream substrates such as RSK, but do not modulate phosphorylation of ERK1/2 by MEK. Crystal structural studies performed by us and others on the pERK1/2 modulating inhibitor SCH772984 suggested that it induces a conformational change in the glycine-rich loop of ERK2, which leads to Tyr36 becoming tucked under the loop and creating a new binding pocket. We hypothesized that this binding mode might underlie the ability of SCH772984 to block the phosphorylation of ERK1/2, and initiated a fragment-based approach to develop novel, orally bioavailable inhibitors that elicit a similar conformational change and also modulate the phosphorylation of ERK1/2. Using screening methods including high-throughput X-ray crystallography and biophysical assays, we identified fragments binding to both the hinge and the inducible pocket of ERK2. Progressive rounds of structure-guided fragment optimization and growing led to an understanding of inhibitor structure determinants required to induce the conformational change in ERK2. These efforts, together with iterative optimization in a screening cascade including measurement of pRSK and pERK levels and antiproliferative activity in RAS and BRAF mutant cells, led to the discovery of a novel series of pERK modulating ERK1/2 inhibitors. The lead compound shows low nanomolar potency in biochemical ERK1/2 assays and an excellent kinome selectivity profile. In BRAF and RAS mutant cell lines, the lead shows low nanomolar cell proliferation IC50 values, while sparing cell lines not driven by the MAPK pathway. The lead exhibits robust antitumor activity upon oral dosing in a range of subcutaneous xenograft models including the mutant BRAF colorectal line Colo205, providing a promising basis for further optimization towards clinical pERK1/2 modulating ERK1/2 inhibitors.
Citation Format: Tom D. Heightman, Valerio Berdini, Hannah Braithwaite, Ildiko Buck, Megan Cassidy, Juan Castro, Aurélie Courtin, James Day, Charlotte East, Lynsey Fazal, Brent Graham, Charlotte Griffiths-Jones, John Lyons, Vanessa Martins, Sandra Muench, Joanne Munck, David Norton, Marc O'Reilly, Nick Palmer, Puja Pathuri, Mike Reader, David Rees, Sharna Rich, Caroline Richardson, Harpreet Saini, Neil Thompson, Nicola Wallis, Hugh Walton, Nicola Wilsher, Alison Woolford, Chris Murray. Fragment-based discovery of a highly potent, orally bioavailable ERK1/2 inhibitor that modulates the phosphorylation and catalytic activity of ERK1/2 [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr B161.
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Affiliation(s)
| | | | | | - Ildiko Buck
- Astex Pharmaceuticals, Inc, Cambridge, United Kingdom
| | - Megan Cassidy
- Astex Pharmaceuticals, Inc, Cambridge, United Kingdom
| | - Juan Castro
- Astex Pharmaceuticals, Inc, Cambridge, United Kingdom
| | | | - James Day
- Astex Pharmaceuticals, Inc, Cambridge, United Kingdom
| | | | - Lynsey Fazal
- Astex Pharmaceuticals, Inc, Cambridge, United Kingdom
| | - Brent Graham
- Astex Pharmaceuticals, Inc, Cambridge, United Kingdom
| | | | - John Lyons
- Astex Pharmaceuticals, Inc, Cambridge, United Kingdom
| | | | - Sandra Muench
- Astex Pharmaceuticals, Inc, Cambridge, United Kingdom
| | - Joanne Munck
- Astex Pharmaceuticals, Inc, Cambridge, United Kingdom
| | - David Norton
- Astex Pharmaceuticals, Inc, Cambridge, United Kingdom
| | - Marc O'Reilly
- Astex Pharmaceuticals, Inc, Cambridge, United Kingdom
| | - Nick Palmer
- Astex Pharmaceuticals, Inc, Cambridge, United Kingdom
| | - Puja Pathuri
- Astex Pharmaceuticals, Inc, Cambridge, United Kingdom
| | - Mike Reader
- Astex Pharmaceuticals, Inc, Cambridge, United Kingdom
| | - David Rees
- Astex Pharmaceuticals, Inc, Cambridge, United Kingdom
| | - Sharna Rich
- Astex Pharmaceuticals, Inc, Cambridge, United Kingdom
| | | | | | - Neil Thompson
- Astex Pharmaceuticals, Inc, Cambridge, United Kingdom
| | - Nicola Wallis
- Astex Pharmaceuticals, Inc, Cambridge, United Kingdom
| | - Hugh Walton
- Astex Pharmaceuticals, Inc, Cambridge, United Kingdom
| | | | | | - Chris Murray
- Astex Pharmaceuticals, Inc, Cambridge, United Kingdom
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13
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Munck JM, Berdini V, Bevan LD, Braithwaite H, Buck IM, Cassidy M, Castro J, Courtin A, Day JE, East C, Fazal L, Graham B, Griffiths-Jones CM, Heightman TD, Hindley CJ, Kidane B, Kucia-Tran J, Lyons JF, Martins V, Muench S, Murray CW, Norton D, O'Reilly M, Palmer N, Pathuri P, Reader M, Rees DC, Rich SJ, Richardson CJ, Saini HK, Shah A, Stanczuk L, Thompson NT, Walton H, Wilsher NE, Woolford AJ, Wallis NG. Abstract B154: Characterization of a novel ERK1/2 inhibitor, which modulates the phosphorylation and catalytic activity of ERK1/2. Mol Cancer Ther 2018. [DOI: 10.1158/1535-7163.targ-17-b154] [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 MAPK pathway is commonly hyper-activated in human cancers due to the occurrence of oncogenic mutations in RAF, RAS and the upregulation of RTKs. The therapeutic potential of MAPK pathway inhibition has been demonstrated by the clinical efficacy of RAF and MEK1/2 (MEK) inhibitors in the treatment of BRAF-mutant melanoma. However, response to such agents is short-lived due to the onset of resistance mechanisms, which in the majority of cases result in the reactivation of ERK1/2 (ERK) signalling. Therefore, the direct targeting of ERK is an attractive therapeutic approach to overcoming the limitations of RAF or MEK inhibitors. Here, we describe a novel, potent, and selective ERK inhibitor, which inhibits both ERK catalytic activity and also the phosphorylation of ERK by MEK. Using fragment-based drug discovery we have developed a selective ERK inhibitor, which inhibits in vitro ERK catalytic activity with a low nM IC50 value. This lead compound has strong antiproliferative effects in a wide range of MAPK-activated cell lines, including the BRAF-mutant cell lines A375 (melanoma) and Colo205 (colorectal), the KRAS-mutant cell lines HCT116 (colorectal), Calu6 (lung) and Panc05.04 (pancreatic), and the NRAS-mutant cell line Ma-mel-27 (melanoma). The lead compound potently inhibits ERK cell signalling. The potent (nM) inhibition of RSK phosphorylation (a direct ERK substrate) was confirmed in A375 (BRAF-mutant melanoma) cells, using MSD analysis. In addition to inhibiting downstream ERK signalling, we demonstrated by ELISA and Western blotting that the lead compound confers a decrease in phospho-ERK levels in both BRAF-mutant and KRAS-mutant cell lines. We investigated the biochemical mechanism of the modulation of ERK phosphorylation in vitro and demonstrated that the compound prevents the phosphorylation of ERK by MEK (at key ERK activation loop residues, T202/Y204), without directly inhibiting MEK activity. The compound was profiled in a range of subcutaneous xenograft models including A375 (BRAF-mutant melanoma) and Calu-6 (KRAS-mutant lung). Once-daily oral dosing of the lead compound conferred significant antitumor activity in a range of in vivo efficacy studies. The compound potently inhibited the phosphorylation of downstream ERK substrates (including RSK) in tumor xenograft tissue. There was a clear relationship between in vivo compound concentrations and the modulation of ERK substrate phosphorylation. Furthermore, as was demonstrated in vitro, we confirmed that in addition to inhibiting ERK catalytic activity the compound potently inhibited the phosphorylation of ERK itself, in both KRAS and BRAF-mutant tumor xenografts. Here, we characterize a novel, highly potent, selective ERK inhibitor, which inhibits both ERK catalytic activity and also the upstream phosphorylation of ERK by MEK. These data support the further optimization of this series of compounds for clinical development.
Citation Format: Joanne M. Munck, Valerio Berdini, Luke D. Bevan, Hannah Braithwaite, Ildiko M. Buck, Megan Cassidy, Juan Castro, Aurelie Courtin, James E. Day, Charlotte East, Lynsey Fazal, Brent Graham, Charlotte M. Griffiths-Jones, Tom D. Heightman, Chris J. Hindley, Birikiti Kidane, Justyna Kucia-Tran, John F. Lyons, Vanessa Martins, Sandra Muench, Chris W. Murray, David Norton, Marc O'Reilly, Nick Palmer, Puja Pathuri, Mike Reader, David C. Rees, Sharna J. Rich, Caroline J. Richardson, Harpreet K. Saini, Alpesh Shah, Lukas Stanczuk, Neil T. Thompson, Hugh Walton, Nicola E. Wilsher, Alison J. Woolford, Nicola G. Wallis. Characterization of a novel ERK1/2 inhibitor, which modulates the phosphorylation and catalytic activity of ERK1/2 [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr B154.
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Affiliation(s)
| | | | | | | | | | | | - Juan Castro
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | | | - James E. Day
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | | | - Lynsey Fazal
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | - Brent Graham
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | | | | | | | | | | | | | | | | | | | - David Norton
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | | | - Nick Palmer
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | - Puja Pathuri
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | - Mike Reader
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | | | | | | | | | - Alpesh Shah
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | | | | | - Hugh Walton
- Astex Pharmaceuticals, Cambridge, United Kingdom
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14
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Lebraud H, Wright DJ, East CE, Holding FP, O'Reilly M, Heightman TD. In-gel activity-based protein profiling of a clickable covalent ERK1/2 inhibitor. Mol Biosyst 2017; 12:2867-74. [PMID: 27385078 DOI: 10.1039/c6mb00367b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In-gel activity-based protein profiling (ABPP) offers rapid assessment of the proteome-wide selectivity and target engagement of a chemical tool. Here we demonstrate the use of the inverse electron demand Diels Alder (IEDDA) click reaction for in-gel ABPP by evaluating the selectivity profile and target engagement of a covalent ERK1/2 probe tagged with a trans-cyclooctene group. The chemical probe was shown to bind covalently to Cys166 of ERK2 using protein MS and X-ray crystallography, and displayed submicromolar GI50s in A375 and HCT116 cells. In both cell lines, the probe demonstrated target engagement and a good selectivity profile at low concentrations, which was lost at higher concentrations. The IEDDA cycloaddition enabled fast and quantitative fluorescent tagging for readout with a high background-to-noise ratio and thereby provides a promising alternative to the commonly used copper catalysed alkyne-azide cycloaddition.
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Affiliation(s)
- Honorine Lebraud
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK.
| | - David J Wright
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK.
| | - Charlotte E East
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK.
| | - Finn P Holding
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK.
| | - Marc O'Reilly
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK.
| | - Tom D Heightman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK.
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15
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Sipthorp J, Lebraud H, Gilley R, Kidger AM, Okkenhaug H, Saba-El-Leil M, Meloche S, Caunt CJ, Cook SJ, Heightman TD. Visualization of Endogenous ERK1/2 in Cells with a Bioorthogonal Covalent Probe. Bioconjug Chem 2017; 28:1677-1683. [PMID: 28449575 DOI: 10.1021/acs.bioconjchem.7b00152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The RAS-RAF-MEK-ERK pathway has been intensively studied in oncology, with RAS known to be mutated in ∼30% of all human cancers. The recent emergence of ERK1/2 inhibitors and their ongoing clinical investigation demands a better understanding of ERK1/2 behavior following small-molecule inhibition. Although fluorescent fusion proteins and fluorescent antibodies are well-established methods of visualizing proteins, we show that ERK1/2 can be visualized via a less-invasive approach based on a two-step process using inverse electron demand Diels-Alder cycloaddition. Our previously reported trans-cyclooctene-tagged covalent ERK1/2 inhibitor was used in a series of imaging experiments following a click reaction with a tetrazine-tagged fluorescent dye. Although limitations were encountered with this approach, endogenous ERK1/2 was successfully imaged in cells, and "on-target" staining was confirmed by over-expressing DUSP5, a nuclear ERK1/2 phosphatase that anchors ERK1/2 in the nucleus.
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Affiliation(s)
- James Sipthorp
- Signalling Laboratory, The Babraham Institute , Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Honorine Lebraud
- Astex Pharmaceuticals , 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Rebecca Gilley
- Signalling Laboratory, The Babraham Institute , Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Andrew M Kidger
- Signalling Laboratory, The Babraham Institute , Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Hanneke Okkenhaug
- Signalling Laboratory, The Babraham Institute , Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Marc Saba-El-Leil
- Institute of Research in Immunology and Cancer and Department of Pharmacology, Université de Montréal , Montréal, Québec, Canada H3C 3J7
| | - Sylvain Meloche
- Institute of Research in Immunology and Cancer and Department of Pharmacology, Université de Montréal , Montréal, Québec, Canada H3C 3J7
| | - Christopher J Caunt
- Department of Biology and Biochemistry, University of Bath , Claverton Down, Bath BA2 7AY, U.K
| | - Simon J Cook
- Signalling Laboratory, The Babraham Institute , Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Tom D Heightman
- Astex Pharmaceuticals , 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
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16
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Tamanini E, Buck IM, Chessari G, Chiarparin E, Day JEH, Frederickson M, Griffiths-Jones CM, Hearn K, Heightman TD, Iqbal A, Johnson CN, Lewis EJ, Martins V, Peakman T, Reader M, Rich SJ, Ward GA, Williams PA, Wilsher NE. Discovery of a Potent Nonpeptidomimetic, Small-Molecule Antagonist of Cellular Inhibitor of Apoptosis Protein 1 (cIAP1) and X-Linked Inhibitor of Apoptosis Protein (XIAP). J Med Chem 2017; 60:4611-4625. [DOI: 10.1021/acs.jmedchem.6b01877] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Emiliano Tamanini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - Ildiko M. Buck
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - Gianni Chessari
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - Elisabetta Chiarparin
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - James E. H. Day
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - Martyn Frederickson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | | | - Keisha Hearn
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - Tom D. Heightman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - Aman Iqbal
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | | | - Edward J. Lewis
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - Vanessa Martins
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - Torren Peakman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - Michael Reader
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - Sharna J. Rich
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - George A. Ward
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - Pamela A. Williams
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - Nicola E. Wilsher
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
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17
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Lebraud H, Wright DJ, Johnson CN, Heightman TD. Protein Degradation by In-Cell Self-Assembly of Proteolysis Targeting Chimeras. ACS Cent Sci 2016; 2:927-934. [PMID: 28058282 PMCID: PMC5200928 DOI: 10.1021/acscentsci.6b00280] [Citation(s) in RCA: 226] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Indexed: 05/03/2023]
Abstract
Selective degradation of proteins by proteolysis targeting chimeras (PROTACs) offers a promising potential alternative to protein inhibition for therapeutic intervention. Current PROTAC molecules incorporate a ligand for the target protein, a linker, and an E3 ubiquitin ligase recruiting group, which bring together target protein and ubiquitinating machinery. Such hetero-bifunctional molecules require significant linker optimization and possess high molecular weight, which can limit cellular permeation, solubility, and other drug-like properties. We show here that the hetero-bifunctional molecule can be formed intracellularly by bio-orthogonal click combination of two smaller precursors. We designed a tetrazine tagged thalidomide derivative which reacts rapidly with a trans-cyclo-octene tagged ligand of the target protein in cells to form a cereblon E3 ligase recruiting PROTAC molecule. The in-cell click-formed proteolysis targeting chimeras (CLIPTACs) were successfully used to degrade two key oncology targets, BRD4 and ERK1/2. ERK1/2 degradation was achieved using a CLIPTAC based on a covalent inhibitor. We expect this approach to be readily extendable to other inhibitor-protein systems because the tagged E3 ligase recruiter is capable of undergoing the click reaction with a suitably tagged ligand of any protein of interest to elicit its degradation.
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18
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Tisi D, Chiarparin E, Tamanini E, Pathuri P, Coyle JE, Hold A, Holding FP, Amin N, Martin ACL, Rich SJ, Berdini V, Yon J, Acklam P, Burke R, Drouin L, Harmer JE, Jeganathan F, van Montfort RLM, Newbatt Y, Tortorici M, Westlake M, Wood A, Hoelder S, Heightman TD. Structure of the Epigenetic Oncogene MMSET and Inhibition by N-Alkyl Sinefungin Derivatives. ACS Chem Biol 2016; 11:3093-3105. [PMID: 27571355 DOI: 10.1021/acschembio.6b00308] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The members of the NSD subfamily of lysine methyl transferases are compelling oncology targets due to the recent characterization of gain-of-function mutations and translocations in several hematological cancers. To date, these proteins have proven intractable to small molecule inhibition. Here, we present initial efforts to identify inhibitors of MMSET (aka NSD2 or WHSC1) using solution phase and crystal structural methods. On the basis of 2D NMR experiments comparing NSD1 and MMSET structural mobility, we designed an MMSET construct with five point mutations in the N-terminal helix of its SET domain for crystallization experiments and elucidated the structure of the mutant MMSET SET domain at 2.1 Å resolution. Both NSD1 and MMSET crystal systems proved resistant to soaking or cocrystallography with inhibitors. However, use of the close homologue SETD2 as a structural surrogate supported the design and characterization of N-alkyl sinefungin derivatives, which showed low micromolar inhibition against both SETD2 and MMSET.
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Affiliation(s)
- Dominic Tisi
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge, United Kingdom CB4 0QA
| | - Elisabetta Chiarparin
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge, United Kingdom CB4 0QA
| | - Emiliano Tamanini
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge, United Kingdom CB4 0QA
| | - Puja Pathuri
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge, United Kingdom CB4 0QA
| | - Joseph E. Coyle
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge, United Kingdom CB4 0QA
| | - Adam Hold
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge, United Kingdom CB4 0QA
| | - Finn P. Holding
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge, United Kingdom CB4 0QA
| | - Nader Amin
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge, United Kingdom CB4 0QA
| | - Agnes C. L. Martin
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge, United Kingdom CB4 0QA
| | - Sharna J. Rich
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge, United Kingdom CB4 0QA
| | - Valerio Berdini
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge, United Kingdom CB4 0QA
| | - Jeff Yon
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge, United Kingdom CB4 0QA
| | - Paul Acklam
- CRUK
Cancer Therapeutics Unit, Institute of Cancer Research, 15 Cotswold
Road, Belmont, Sutton, Surrey, United Kingdom SM2 5NG
| | - Rosemary Burke
- CRUK
Cancer Therapeutics Unit, Institute of Cancer Research, 15 Cotswold
Road, Belmont, Sutton, Surrey, United Kingdom SM2 5NG
| | - Ludovic Drouin
- CRUK
Cancer Therapeutics Unit, Institute of Cancer Research, 15 Cotswold
Road, Belmont, Sutton, Surrey, United Kingdom SM2 5NG
| | - Jenny E. Harmer
- CRUK
Cancer Therapeutics Unit, Institute of Cancer Research, 15 Cotswold
Road, Belmont, Sutton, Surrey, United Kingdom SM2 5NG
| | - Fiona Jeganathan
- CRUK
Cancer Therapeutics Unit, Institute of Cancer Research, 15 Cotswold
Road, Belmont, Sutton, Surrey, United Kingdom SM2 5NG
| | - Rob L. M. van Montfort
- CRUK
Cancer Therapeutics Unit, Institute of Cancer Research, 15 Cotswold
Road, Belmont, Sutton, Surrey, United Kingdom SM2 5NG
| | - Yvette Newbatt
- CRUK
Cancer Therapeutics Unit, Institute of Cancer Research, 15 Cotswold
Road, Belmont, Sutton, Surrey, United Kingdom SM2 5NG
| | - Marcello Tortorici
- CRUK
Cancer Therapeutics Unit, Institute of Cancer Research, 15 Cotswold
Road, Belmont, Sutton, Surrey, United Kingdom SM2 5NG
| | - Maura Westlake
- CRUK
Cancer Therapeutics Unit, Institute of Cancer Research, 15 Cotswold
Road, Belmont, Sutton, Surrey, United Kingdom SM2 5NG
| | - Amy Wood
- CRUK
Cancer Therapeutics Unit, Institute of Cancer Research, 15 Cotswold
Road, Belmont, Sutton, Surrey, United Kingdom SM2 5NG
| | - Swen Hoelder
- CRUK
Cancer Therapeutics Unit, Institute of Cancer Research, 15 Cotswold
Road, Belmont, Sutton, Surrey, United Kingdom SM2 5NG
| | - Tom D. Heightman
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge, United Kingdom CB4 0QA
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19
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Sekirnik Née Measures AR, Hewings DS, Theodoulou NH, Jursins L, Lewendon KR, Jennings LE, Rooney TPC, Heightman TD, Conway SJ. Isoxazole-Derived Amino Acids are Bromodomain-Binding Acetyl-Lysine Mimics: Incorporation into Histone H4 Peptides and Histone H3. Angew Chem Int Ed Engl 2016; 55:8353-7. [PMID: 27264992 PMCID: PMC5089653 DOI: 10.1002/anie.201602908] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/08/2016] [Indexed: 02/06/2023]
Abstract
A range of isoxazole‐containing amino acids was synthesized that displaced acetyl‐lysine‐containing peptides from the BAZ2A, BRD4(1), and BRD9 bromodomains. Three of these amino acids were incorporated into a histone H4‐mimicking peptide and their affinity for BRD4(1) was assessed. Affinities of the isoxazole‐containing peptides are comparable to those of a hyperacetylated histone H4‐mimicking cognate peptide, and demonstrated a dependence on the position at which the unnatural residue was incorporated. An isoxazole‐based alkylating agent was developed to selectively alkylate cysteine residues in situ. Selective monoalkylation of a histone H4‐mimicking peptide, containing a lysine to cysteine residue substitution (K12C), resulted in acetyl‐lysine mimic incorporation, with high affinity for the BRD4 bromodomain. The same technology was used to alkylate a K18C mutant of histone H3.
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Affiliation(s)
| | - David S Hewings
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Natalie H Theodoulou
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Lukass Jursins
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Katie R Lewendon
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Laura E Jennings
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Timothy P C Rooney
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Tom D Heightman
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.
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20
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Sekirnik née Measures AR, Hewings DS, Theodoulou NH, Jursins L, Lewendon KR, Jennings LE, Rooney TPC, Heightman TD, Conway SJ. Isoxazole-Derived Amino Acids are Bromodomain-Binding Acetyl-Lysine Mimics: Incorporation into Histone H4 Peptides and Histone H3. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602908] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | - David S. Hewings
- Department of Chemistry, Chemistry Research Laboratory; University of Oxford; Mansfield Road Oxford OX1 3TA UK
| | - Natalie H. Theodoulou
- Department of Chemistry, Chemistry Research Laboratory; University of Oxford; Mansfield Road Oxford OX1 3TA UK
| | - Lukass Jursins
- Department of Chemistry, Chemistry Research Laboratory; University of Oxford; Mansfield Road Oxford OX1 3TA UK
| | - Katie R. Lewendon
- Department of Chemistry, Chemistry Research Laboratory; University of Oxford; Mansfield Road Oxford OX1 3TA UK
| | - Laura E. Jennings
- Department of Chemistry, Chemistry Research Laboratory; University of Oxford; Mansfield Road Oxford OX1 3TA UK
| | - Timothy P. C. Rooney
- Department of Chemistry, Chemistry Research Laboratory; University of Oxford; Mansfield Road Oxford OX1 3TA UK
| | - Tom D. Heightman
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium; University of Oxford, Old Road Campus Research Building; Roosevelt Drive Oxford OX3 7DQ UK
| | - Stuart J. Conway
- Department of Chemistry, Chemistry Research Laboratory; University of Oxford; Mansfield Road Oxford OX1 3TA UK
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21
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Davies TG, Wixted WE, Coyle JE, Griffiths-Jones C, Hearn K, McMenamin R, Norton D, Rich SJ, Richardson C, Saxty G, Willems HMG, Woolford AJA, Cottom JE, Kou JP, Yonchuk JG, Feldser HG, Sanchez Y, Foley JP, Bolognese BJ, Logan G, Podolin PL, Yan H, Callahan JF, Heightman TD, Kerns JK. Monoacidic Inhibitors of the Kelch-like ECH-Associated Protein 1: Nuclear Factor Erythroid 2-Related Factor 2 (KEAP1:NRF2) Protein–Protein Interaction with High Cell Potency Identified by Fragment-Based Discovery. J Med Chem 2016; 59:3991-4006. [DOI: 10.1021/acs.jmedchem.6b00228] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Thomas G. Davies
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | - William E. Wixted
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Joseph E. Coyle
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | | | - Keisha Hearn
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | - Rachel McMenamin
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | - David Norton
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | - Sharna J. Rich
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | | | - Gordon Saxty
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | | | | | - Joshua E. Cottom
- GlaxoSmithKline
Pharmaceuticals, 1250 South Collegeville
Road, Collegeville, Pennsylvania 19426, United States
| | - Jen-Pyng Kou
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - John G. Yonchuk
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Heidi G. Feldser
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Yolanda Sanchez
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Joseph P. Foley
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Brian J. Bolognese
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Gregory Logan
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Patricia L. Podolin
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Hongxing Yan
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - James F. Callahan
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Tom D. Heightman
- Astex Pharmaceuticals, 436 Cambridge
Science Park, Cambridge CB4 0QA, U.K
| | - Jeffrey K. Kerns
- GlaxoSmithKline
Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
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22
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Abstract
The approval of DNA methylation inhibitors azacytidine and decitabine for the treatment of myelodysplastic syndromes and acute myeloid leukaemia has demonstrated that modulation of relatively broad epigenetic regulatory processes can show beneficial efficacy/safety profiles in defined patient groups. This chapter will focus on the biochemical mechanisms controlling DNA methylation, consequences of aberrant DNA methylation in complex chronic diseases, existing modulators of DNA methylation used in the clinic, and opportunities for new drugs targeting this central epigenetic mechanism.
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Affiliation(s)
- Tom D. Heightman
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - Michael McCullar
- Astex Pharmaceuticals Inc. 4140 Dublin Boulevard, Suite 200 Dublin CA 94568 USA
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23
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Skidmore J, Heer J, Johnson CN, Norton D, Redshaw S, Sweeting J, Hurst D, Cridland A, Vesey D, Wall I, Ahmed M, Rivers D, Myatt J, Giblin G, Philpott K, Kumar U, Stevens A, Bit RA, Haynes A, Taylor S, Watson R, Witherington J, Demont E, Heightman TD. Optimization of sphingosine-1-phosphate-1 receptor agonists: effects of acidic, basic, and zwitterionic chemotypes on pharmacokinetic and pharmacodynamic profiles. J Med Chem 2014; 57:10424-42. [PMID: 25431977 DOI: 10.1021/jm5010336] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The efficacy of the recently approved drug fingolimod (FTY720) in multiple sclerosis patients results from the action of its phosphate metabolite on sphingosine-1-phosphate S1P1 receptors, while a variety of side effects have been ascribed to its S1P3 receptor activity. Although S1P and phospho-fingolimod share the same structural elements of a zwitterionic headgroup and lipophilic tail, a variety of chemotypes have been found to show S1P1 receptor agonism. Here we describe a study of the tolerance of the S1P1 and S1P3 receptors toward bicyclic heterocycles of systematically varied shape and connectivity incorporating acidic, basic, or zwitterionic headgroups. We compare their physicochemical properties, their performance in in vitro and in vivo pharmacokinetic models, and their efficacy in peripheral lymphocyte lowering. The campaign resulted in the identification of several potent S1P1 receptor agonists with good selectivity vs S1P3 receptors, efficacy at <1 mg/kg oral doses, and developability properties suitable for progression into preclinical development.
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Affiliation(s)
- John Skidmore
- Neurology Center of Excellence for Drug Discovery, GlaxoSmithKline , New Frontiers Science Park, Harlow CM19 5AW, U.K
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24
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Kanno T, Kanno Y, LeRoy G, Campos E, Sun HW, Brooks SR, Vahedi G, Heightman TD, Garcia BA, Reinberg D, Siebenlist U, O’Shea JJ, Ozato K. BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones. Nat Struct Mol Biol 2014; 21:1047-57. [PMID: 25383670 PMCID: PMC4720983 DOI: 10.1038/nsmb.2912] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 10/06/2014] [Indexed: 02/07/2023]
Abstract
Small-molecule BET inhibitors interfere with the epigenetic interactions between acetylated histones and the bromodomains of the BET family proteins, including BRD4, and they potently inhibit growth of malignant cells by targeting cancer-promoting genes. BRD4 interacts with the pause-release factor P-TEFb and has been proposed to release RNA polymerase II (Pol II) from promoter-proximal pausing. We show that BRD4 occupies widespread genomic regions in mouse cells and directly stimulates elongation of both protein-coding transcripts and noncoding enhancer RNAs (eRNAs), in a manner dependent on bromodomain function. BRD4 interacts with elongating Pol II complexes and assists Pol II in progression through hyperacetylated nucleosomes by interacting with acetylated histones via bromodomains. On active enhancers, the BET inhibitor JQ1 antagonizes BRD4-associated eRNA synthesis. Thus, BRD4 is involved in multiple steps of the transcription hierarchy, primarily by facilitating transcript elongation both at enhancers and on gene bodies independently of P-TEFb.
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Affiliation(s)
- Tomohiko Kanno
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
- Program in Genomics of Differentiation, National Institutes of Child Health and Human Development, Bethesda, MD, USA
| | - Yuka Kanno
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Gary LeRoy
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY, USA
| | - Eric Campos
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY, USA
| | - Hong-Wei Sun
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Stephen R Brooks
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Golnaz Vahedi
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Tom D Heightman
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, UK
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY, USA
| | - Ulrich Siebenlist
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - John J O’Shea
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Keiko Ozato
- Program in Genomics of Differentiation, National Institutes of Child Health and Human Development, Bethesda, MD, USA
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25
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Heightman TD. Abstract SY05-01: Fragment-based drug discovery: Less is more. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-sy05-01] [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, fragment-based drug discovery (FBDD) has become increasingly widely used across industry and academia, as highlighted recently (1). This is likely driven by the successful identification of leads for targets considered intractable using conventional screening strategies, in addition to delivering leads with improved physicochemical properties for more tractable targets such as kinases (2).
The fundamental concept of fragment screening is to use simpler molecules so that the chemical space can be sampled much more efficiently than is possible when using molecules of greater complexity (3). One consequence of screening smaller, simpler fragments is that their affinity is expected to be relatively low (>1 mM), given the limited numbers of potential interactions that they can make with the protein, and the detection of low-potency fragment hits presents substantial technical challenges. However, although weak in potency, fragment hits make high-quality interactions with the protein as they must overcome a substantial entropic barrier to binding, relative to their size, and their binding thereby frequently occurs with high efficiencies.
We now have experience of over 30 high-throughput crystallographic and biophysical fragment screens against a broad range of protein classes, and our results support the view that less complex molecules give a higher hit rate. This rich dataset of protein-fragment interactions has allowed continuous optimization of our fragment library, to maximize both success in fragment screening campaigns, and synthetic efficiency during fragment development. In addition, the ability to routinely produce multiple iterations of fast-turnaround crystallography has proven invaluable in guiding medicinal chemistry optimization, allowing parsimonious building of affinity, which provides drug candidates with enhanced ligand efficiency likely to minimize attrition in development.
The success of the approach will be illustrated by the fragment-based discovery of novel dual inhibitors of protein-protein interactions involving XIAP and cIAP1.
XIAP and cIAP1 are members of the inhibitor of apoptosis protein (IAP) family, a class of proteins that can down-regulate the apoptosis process by inhibiting caspases and other apoptotic factors (4). A defining feature of these proteins is the presence of three Baculoviral IAP Repeat (BIR) domains in their sequence. SMAC (second mitochondrial activator of caspases) is released by mitochondria in response to apoptotic stimuli and deactivates the function of IAPs through binding of its N-terminal region (AVPI) to the IAP-BIR domains. This event disrupts protein-protein interactions between IAPs and caspases and promotes apoptosis. It has recently been demonstrated that dual antagonism of both XIAP and cIAP1 is required to achieve a strong apoptotic response (5).
Several companies and academic groups have active programs developing SMAC peptidomimetic compounds for the treatment of cancer. These compounds are based on the key alanine motif in AVPI which engenders cIAP1 selectivity (IC50 values for AVPI vs XIAP-BIR3 and cIAP1-BIR3 are 0.3 uM and 0.016 uM respectively).
Our fragment-based screening approach, PyramidTM, enabled us to identify a non-alanine fragment which binds with similar affinity for both XIAP and cIAP1. Hit optimisation using a structure-based approach led to the discovery of a dual XIAP and cIAP1 antagonist with potent in vivo pharmacodynamic activity when delivered orally in a mouse xenograft model. High concentrations of the compound were measured in tumor and plasma over a 24 h period which ensured potent antagonism of both XIAP and cIAP1. Induction of apoptosis biomarkers (cleaved PARP, cleaved caspase-3) and strong inhibition of tumor growth were also observed for this new class of inhibitors.
References
1. M. Baker, Nature Rev. Drug Discov. 2013, 12, 5.
2. P. Leeson & S. St-Gallay, Nature Reviews Drug Discovery 2011, 10, 749.
3. M.M. Hann, A.R. Leach & G. Harper, J. Chem. Inf. Comput. Sci. 2001, 41, 856.
4. S. Fulda & D. Vucic, Nat. Rev. Drug Disc. 2012, 11, 109.
5. C. Ndubaku et al, ACS Chem. Biol. 2009, 4, 557.
Citation Format: Tom D. Heightman. Fragment-based drug discovery: Less is more. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr SY05-01. doi:10.1158/1538-7445.AM2014-SY05-01
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Rooney TPC, Filippakopoulos P, Fedorov O, Picaud S, Cortopassi WA, Hay DA, Martin S, Tumber A, Rogers CM, Philpott M, Wang M, Thompson AL, Heightman TD, Pryde DC, Cook A, Paton RS, Müller S, Knapp S, Brennan PE, Conway SJ. A Series of Potent CREBBP Bromodomain Ligands Reveals an Induced-Fit Pocket Stabilized by a Cation-π Interaction. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402750] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Rooney TPC, Filippakopoulos P, Fedorov O, Picaud S, Cortopassi WA, Hay DA, Martin S, Tumber A, Rogers CM, Philpott M, Wang M, Thompson AL, Heightman TD, Pryde DC, Cook A, Paton RS, Müller S, Knapp S, Brennan PE, Conway SJ. A series of potent CREBBP bromodomain ligands reveals an induced-fit pocket stabilized by a cation-π interaction. Angew Chem Int Ed Engl 2014; 53:6126-30. [PMID: 24821300 PMCID: PMC4298791 DOI: 10.1002/anie.201402750] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Indexed: 12/04/2022]
Abstract
The benzoxazinone and dihydroquinoxalinone fragments were employed as novel acetyl lysine mimics in the development of CREBBP bromodomain ligands. While the benzoxazinone series showed low affinity for the CREBBP bromodomain, expansion of the dihydroquinoxalinone series resulted in the first potent inhibitors of a bromodomain outside the BET family. Structural and computational studies reveal that an internal hydrogen bond stabilizes the protein-bound conformation of the dihydroquinoxalinone series. The side chain of this series binds in an induced-fit pocket forming a cation–π interaction with R1173 of CREBBP. The most potent compound inhibits binding of CREBBP to chromatin in U2OS cells.
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Affiliation(s)
- Timothy P C Rooney
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA (UK) http://conway.chem.ox.ac.uk/
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Howard S, Amin N, Benowitz AB, Chiarparin E, Cui H, Deng X, Heightman TD, Holmes DJ, Hopkins A, Huang J, Jin Q, Kreatsoulas C, Martin ACL, Massey F, McCloskey L, Mortenson PN, Pathuri P, Tisi D, Williams PA. Fragment-based discovery of 6-azaindazoles as inhibitors of bacterial DNA ligase. ACS Med Chem Lett 2013; 4:1208-12. [PMID: 24900632 DOI: 10.1021/ml4003277] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 10/10/2013] [Indexed: 02/06/2023] Open
Abstract
Herein we describe the application of fragment-based drug design to bacterial DNA ligase. X-ray crystallography was used to guide structure-based optimization of a fragment-screening hit to give novel, nanomolar, AMP-competitive inhibitors. The lead compound 13 showed antibacterial activity across a range of pathogens. Data to demonstrate mode of action was provided using a strain of S. aureus, engineered to overexpress DNA ligase.
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Affiliation(s)
- Steven Howard
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Nader Amin
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Andrew B. Benowitz
- GlaxoSmithKline, Infectious Diseases TAU, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Elisabetta Chiarparin
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Haifeng Cui
- GlaxoSmithKline, Infectious Diseases TAU, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Xiaodong Deng
- GlaxoSmithKline, Infectious Diseases TAU, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Tom D. Heightman
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - David J. Holmes
- GlaxoSmithKline, Infectious Diseases TAU, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Anna Hopkins
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Jianzhong Huang
- GlaxoSmithKline, Infectious Diseases TAU, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Qi Jin
- GlaxoSmithKline, Infectious Diseases TAU, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Constantine Kreatsoulas
- GlaxoSmithKline, Infectious Diseases TAU, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Agnes C. L. Martin
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Frances Massey
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Lynn McCloskey
- GlaxoSmithKline, Infectious Diseases TAU, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Paul N. Mortenson
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Puja Pathuri
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Dominic Tisi
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Pamela A. Williams
- Astex
Pharmaceuticals Inc., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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Wilson DM, Apps J, Bailey N, Bamford MJ, Beresford IJ, Briggs MA, Calver AR, Crook B, Davis RP, Davis S, Dean DK, Harris L, Heightman TD, Panchal T, Parr CA, Quashie N, Steadman JG, Schogger J, Sehmi SS, Stean TO, Takle AK, Trail BK, White T, Witherington J, Worby A, Medhurst AD. The discovery of the benzazepine class of histamine H3 receptor antagonists. Bioorg Med Chem Lett 2013; 23:6897-901. [DOI: 10.1016/j.bmcl.2013.09.089] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 09/24/2013] [Accepted: 09/27/2013] [Indexed: 11/16/2022]
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Sarai N, Nimura K, Tamura T, Kanno T, Patel MC, Heightman TD, Ura K, Ozato K. WHSC1 links transcription elongation to HIRA-mediated histone H3.3 deposition. EMBO J 2013; 32:2392-406. [PMID: 23921552 DOI: 10.1038/emboj.2013.176] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 07/10/2013] [Indexed: 01/22/2023] Open
Abstract
Actively transcribed genes are enriched with the histone variant H3.3. Although H3.3 deposition has been linked to transcription, mechanisms controlling this process remain elusive. We investigated the role of the histone methyltransferase Wolf-Hirschhorn syndrome candidate 1 (WHSC1) (NSD2/MMSET) in H3.3 deposition into interferon (IFN) response genes. IFN treatment triggered robust H3.3 incorporation into activated genes, which continued even after cessation of transcription. Likewise, UV radiation caused H3.3 deposition in UV-activated genes. However, in Whsc1(-/-) cells IFN- or UV-triggered H3.3 deposition was absent, along with a marked reduction in IFN- or UV-induced transcription. We found that WHSC1 interacted with the bromodomain protein 4 (BRD4) and the positive transcription elongation factor b (P-TEFb) and facilitated transcriptional elongation. WHSC1 also associated with HIRA, the H3.3-specific histone chaperone, independent of BRD4 and P-TEFb. WHSC1 and HIRA co-occupied IFN-stimulated genes and supported prolonged H3.3 incorporation, leaving a lasting transcriptional mark. Our results reveal a previously unrecognized role of WHSC1, which links transcriptional elongation and H3.3 deposition into activated genes through two molecularly distinct pathways.
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Affiliation(s)
- Naoyuki Sarai
- Program in Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Hay D, Fedorov O, Filippakopoulos P, Martin S, Philpott M, Picaud S, Hewings DS, Uttakar S, Heightman TD, Conway SJ, Knapp S, Brennan PE. The design and synthesis of 5- and 6-isoxazolylbenzimidazoles as selective inhibitors of the BET bromodomains. Medchemcomm 2013; 4:140-144. [PMID: 26682033 DOI: 10.1039/c2md20189e] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Simple 1-substituted 5- and 6-isoxazolyl-benzimidazoles have been shown to be potent inhibitors of the BET bromodomains with selectivity over the related bromodomain of CBP. The reported inhibitors were prepared from simple starting materials in two steps followed by separation of the regioisomers or regioselectively in three steps.
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Affiliation(s)
- Duncan Hay
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Oleg Fedorov
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Sarah Martin
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Martin Philpott
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - David S Hewings
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Sagar Uttakar
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Tom D Heightman
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Stefan Knapp
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Paul E Brennan
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
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Spencer J, Amin J, Boddiboyena R, Packham G, Cavell BE, Syed Alwi SS, Paranal RM, Heightman TD, Wang M, Marsden B, Coxhead P, Guille M, Tizzard GJ, Coles SJ, Bradner. JE. Click JAHAs: conformationally restricted ferrocene-based histone deacetylase inhibitors. Med Chem Commun 2012. [DOI: 10.1039/c1md00203a] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ferrocene analogue 4b had an IC50 = 4 nM (HDAC1), 180 nM (HDAC8) and was effective in a Xenopus model of tubulin deacetylation. Analogue 4a displayed mainly μM IC50 values against HDACs apart from HDAC6 (IC50 = 69 nM).
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Demont EH, Arpino S, Bit RA, Campbell CA, Deeks N, Desai S, Dowell SJ, Gaskin P, Gray JRJ, Harrison LA, Haynes A, Heightman TD, Holmes DS, Humphreys PG, Kumar U, Morse MA, Osborne GJ, Panchal T, Philpott KL, Taylor S, Watson R, Willis R, Witherington J. Discovery of a brain-penetrant S1P₃-sparing direct agonist of the S1P₁ and S1P₅ receptors efficacious at low oral dose. J Med Chem 2011; 54:6724-33. [PMID: 21838322 DOI: 10.1021/jm200609t] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
2-Amino-2-(4-octylphenethyl)propane-1,3-diol 1 (fingolimod, FTY720) has been recently marketed in the United States for the treatment of patients with remitting relapsing multiple sclerosis (RRMS). Its efficacy has been primarily linked to the agonism on T cells of S1P(1), one of the five sphingosine 1-phosphate (S1P) G-protein-coupled receptors, while its cardiovascular side effects have been associated with activity at S1P(3). Emerging data suggest that the ability of this molecule to cross the blood-brain barrier and to interact with both S1P(1) and S1P(5) in the central nervous system (CNS) may contribute to its efficacy in treating patients with RRMS. We have recently disclosed the structure of an advanced, first generation S1P(3)-sparing S1P(1) agonist, a zwitterion with limited CNS exposure. In this Article, we highlight our strategy toward the identification of CNS-penetrant S1P(3)-sparing S1P(1) and S1P(5) agonists resulting in the discovery of 5-(3-{2-[2-hydroxy-1-(hydroxymethyl)ethyl]-5-methyl-1,2,3,4-tetrahydro-6-isoquinolinyl}-1,2,4-oxadiazol-5-yl)-2-[(1-methylethyl)oxy]benzonitrile 15. Its exceptional in vivo potency and good pharmacokinetic properties translate into a very low predicted therapeutic dose in human (<1 mg p.o. once daily).
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Affiliation(s)
- Emmanuel H Demont
- Immuno Inflammation Center of Excellence for Drug Discovery, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, United Kingdom.
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Hewings DS, Wang M, Philpott M, Fedorov O, Uttarkar S, Filippakopoulos P, Picaud S, Vuppusetty C, Marsden B, Knapp S, Conway SJ, Heightman TD. 3,5-dimethylisoxazoles act as acetyl-lysine-mimetic bromodomain ligands. J Med Chem 2011; 54:6761-70. [PMID: 21851057 PMCID: PMC3188285 DOI: 10.1021/jm200640v] [Citation(s) in RCA: 183] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
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Histone–lysine acetylation is a vital chromatin post-translational modification involved in the epigenetic regulation of gene transcription. Bromodomains bind acetylated lysines, acting as readers of the histone-acetylation code. Competitive inhibitors of this interaction have antiproliferative and anti-inflammatory properties. With 57 distinct bromodomains known, the discovery of subtype-selective inhibitors of the histone–bromodomain interaction is of great importance. We have identified the 3,5-dimethylisoxazole moiety as a novel acetyl-lysine bioisostere, which displaces acetylated histone-mimicking peptides from bromodomains. Using X-ray crystallographic analysis, we have determined the interactions responsible for the activity and selectivity of 4-substituted 3,5-dimethylisoxazoles against a selection of phylogenetically diverse bromodomains. By exploiting these interactions, we have developed compound 4d, which has IC50 values of <5 μM for the bromodomain-containing proteins BRD2(1) and BRD4(1). These compounds are promising leads for the further development of selective probes for the bromodomain and extra C-terminal domain (BET) family and CREBBP bromodomains.
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Affiliation(s)
- David S Hewings
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
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Abstract
Abnormal levels of DNA methylation and/or histone modifications are observed in patients with a wide variety of chronic diseases. Methylation of lysines within histone tails is a key modification that contributes to increased gene expression or repression depending on the specific residue and degree of methylation, which is in turn controlled by the interplay of lysine methyl transferases and demethylases. Drugs that target these and other enzymes controlling chromatin modifications can modulate the expression of clusters of genes, potentially offering higher therapeutic efficacy than classical agents acting on downstream biochemical pathways that are susceptible to degeneracy. Lysine demethylases, first discovered in 2004, are the subject of increasing interest as therapeutic targets. This review provides an overview of recent findings implicating lysine demethylases in a range of therapeutic areas including oncology, immunoinflammation, metabolic disorders, neuroscience, virology and regenerative medicine, together with a summary of recent advances in structural biology and small molecule inhibitor discovery, supporting the tractability of the protein family for the development of selective druglike inhibitors.
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Affiliation(s)
- Tom D Heightman
- Structural Genomics Consortium, Oxford University, Roosevelt Drive, Oxford OX3 7DQ, UK
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Philpott M, Yang J, Tumber T, Fedorov O, Uttarkar S, Filippakopoulos P, Picaud S, Keates T, Felletar I, Ciulli A, Knapp S, Heightman TD. Bromodomain-peptide displacement assays for interactome mapping and inhibitor discovery. Mol Biosyst 2011; 7:2899-908. [PMID: 21804994 DOI: 10.1039/c1mb05099k] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Histone lysine acetylation is a key component of epigenetic regulation of gene transcription. Bromodomains, found in histone acetyl transferases and other chromatin-associated proteins, bind selectively to acetylated lysines, acting as "readers" of the histone code, and have recently been shown to contain a druggable binding pocket. Here we report the development of high-throughput assays that quantify the binding of bromodomains to acetylated histone peptides. We have used these assays to screen for histone binding partners of as yet uncharacterized bromodomains, adding to current knowledge of the histone code and expanding the repertoire of assays for chemical probe discovery. We have also demonstrated that these assays can be used to detect small molecule binding from the very weak to the nanomolar range. This assay methodology is thereby anticipated to provide the basis both for broader interactome profiling and for small molecule inhibitor discovery.
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Affiliation(s)
- Martin Philpott
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
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Luo X, Liu Y, Kubicek S, Myllyharju J, Tumber A, Ng S, Che KH, Podoll J, Heightman TD, Oppermann U, Schreiber SL, Wang X. A selective inhibitor and probe of the cellular functions of Jumonji C domain-containing histone demethylases. J Am Chem Soc 2011; 133:9451-6. [PMID: 21585201 DOI: 10.1021/ja201597b] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Histone methylations are important chromatin marks that regulate gene expression, genomic stability, DNA repair, and genomic imprinting. Histone demethylases are the most recent family of histone-modifying enzymes discovered. Here, we report the characterization of a small-molecule inhibitor of Jumonji C domain-containing histone demethylases. The inhibitor derives from a structure-based design and preferentially inhibits the subfamily of trimethyl lysine demethylases. Its methyl ester prodrug, methylstat, selectively inhibits Jumonji C domain-containing his-tone demethylases in cells and may be a useful small-molecule probe of chromatin and its role in epigenetics.
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Affiliation(s)
- Xuelai Luo
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
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Spencer J, Amin J, Wang M, Packham G, Alwi SSS, Tizzard GJ, Coles SJ, Paranal RM, Bradner JE, Heightman TD. Synthesis and Biological Evaluation of JAHAs: Ferrocene-Based Histone Deacetylase Inhibitors. ACS Med Chem Lett 2011; 2:358-362. [PMID: 21572592 PMCID: PMC3093745 DOI: 10.1021/ml100295v] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [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: 12/09/2010] [Accepted: 03/02/2011] [Indexed: 12/25/2022] Open
Abstract
N(1)-Hydroxy-N(8)-ferrocenyloctanediamide, JAHA (7), an organometallic analogue of SAHA containing a ferrocenyl group as a phenyl bioisostere, displays nanomolar inhibition of class I HDACs, excellent selectivity over class IIa HDACs, and anticancer action in intact cells (IC(50) = 2.4 μM, MCF7 cell line). Molecular docking studies of 7 in HDAC8 (a,b) suggested that the ferrocenyl moiety in 7 can overlap with the aryl cap of SAHA and should display similar HDAC inhibition, which was borne out in an in vitro assay (IC(50) values against HDAC8 (μM, SD in parentheses): SAHA, 1.41 (0.15); 7, 1.36 (0.16). Thereafter, a small library of related JAHA analogues has been synthesized, and preliminary SAR studies are presented. IC(50) values as low as 90 pM toward HDAC6 (class IIb) have been determined, highlighting the excellent potential of JAHAs as bioinorganic probes.
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Affiliation(s)
- John Spencer
- School of Science at Medway, University of Greenwich, Chatham, ME4 4TB, United Kingdom
| | - Jahangir Amin
- School of Science at Medway, University of Greenwich, Chatham, ME4 4TB, United Kingdom
| | - Minghua Wang
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Old Road Campus, Roosevelt Drive, Headington, Oxford OX3 7DQ, United Kingdom
| | - Graham Packham
- Cancer Research UK Centre, University of Southampton, Faculty of Medicine, Mailpoint 824, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Sharifah S. Syed Alwi
- Cancer Research UK Centre, University of Southampton, Faculty of Medicine, Mailpoint 824, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, United Kingdom
| | - Graham J. Tizzard
- UK National Crystallography Service, School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, United Kingdom
| | - Simon J. Coles
- UK National Crystallography Service, School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, United Kingdom
| | - Ronald M. Paranal
- Dana-Farber Cancer Institute, 44 Binney Street, Dana Building, D510D, Boston, Massachusetts 02115, United States
| | - James E. Bradner
- Dana-Farber Cancer Institute, 44 Binney Street, Dana Building, D510D, Boston, Massachusetts 02115, United States
| | - Tom D. Heightman
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Old Road Campus, Roosevelt Drive, Headington, Oxford OX3 7DQ, United Kingdom
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Chang KH, King ONF, Tumber A, Woon ECY, Heightman TD, McDonough MA, Schofield CJ, Rose NR. Inhibition of histone demethylases by 4-carboxy-2,2'-bipyridyl compounds. ChemMedChem 2011; 6:759-764. [PMID: 21412984 DOI: 10.1002/cmdc.201100026] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Indexed: 11/06/2022]
Affiliation(s)
- Kai-Hsuan Chang
- Chemistry Research Laboratory, University of Oxford Oxford, OX1 3TA, United Kingdom
| | - Oliver N F King
- Chemistry Research Laboratory, University of Oxford Oxford, OX1 3TA, United Kingdom
| | - Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, United Kingdom
| | - Esther C Y Woon
- Chemistry Research Laboratory, University of Oxford Oxford, OX1 3TA, United Kingdom
| | - Tom D Heightman
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, United Kingdom
| | - Michael A McDonough
- Chemistry Research Laboratory, University of Oxford Oxford, OX1 3TA, United Kingdom
| | | | - Nathan R Rose
- Chemistry Research Laboratory, University of Oxford Oxford, OX1 3TA, United Kingdom
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Abstract
INTRODUCTION Epigenetics describes the phenomenon of heritable changes in gene regulation governed by non-Mendelian processes, primarily through biochemical modifications to chromatin that occur during cell differentiation and development. Abnormal levels of DNA and/or histone modifications are observed in patients with a wide variety of chronic diseases. Drugs that target the proteins controlling these chromatin modifications can modulate the expression of clusters of genes, potentially offering higher therapeutic efficacy than classical agents with single target pharmacologies that are susceptible to biochemical pathway degeneracy. AREAS COVERED This article reviews research characterizing dysregulation of epigenetic processes in cancer, immuno-inflammatory, psychiatric, neurological, metabolic and virology disease areas, and summarizes recent developments in identifying small molecule modulators that are being used to inform target discovery and initiate drug discovery projects. EXPERT OPINION There are numerous potential opportunities for epigenetic modulators in treating a wide range of chronic diseases; however, the field is complex, involving > 300 proteins, and much work is still required to provide tools to unravel the functions of individual proteins, particularly in vivo. This groundwork is essential to allow the drug discovery community to focus on those epigenetic proteins most likely to be suitable targets for safe, efficacious new therapies.
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Affiliation(s)
- Tom D Heightman
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Cambridge CB4 0QA, UK.
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Thalhammer A, Mecinović J, Loenarz C, Tumber A, Rose NR, Heightman TD, Schofield CJ. Inhibition of the histone demethylase JMJD2E by 3-substituted pyridine 2,4-dicarboxylates. Org Biomol Chem 2011; 9:127-35. [PMID: 21076780 PMCID: PMC4733660 DOI: 10.1039/c0ob00592d] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Based on structural analysis of the human 2-oxoglutarate (2OG) dependent JMJD2 histone N(ε)-methyl lysyl demethylase family, 3-substituted pyridine 2,4-dicarboxylic acids were identified as potential inhibitors with possible selectivity over other human 2OG oxygenases. Microwave-assisted palladium-catalysed cross coupling methodology was developed to install a diverse set of substituents on the sterically demanding C-3 position of a pyridine 2,4-dicarboxylate scaffold. The subsequently prepared di-acids were tested for in vitro inhibition of the histone demethylase JMJD2E and another human 2OG oxygenase, prolyl-hydroxylase domain isoform 2 (PHD2, EGLN1). A subset of substitution patterns yielded inhibitors with selectivity for JMJD2E over PHD2, demonstrating that structure-based inhibitor design can enable selective inhibition of histone demethylases over related human 2OG oxygenases.
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Affiliation(s)
- Armin Thalhammer
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
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Abstract
Epigenetics describes the phenomenon of heritable changes in gene regulation that are governed by non-Mendelian processes, primarily through biochemical modifications to chromatin structure that occur during cell development and differentiation. Numerous lines of evidence link abnormal levels of chromatin modifications (either to DNA, histones, or both) in patients with a wide variety of diseases including cancer, psychiatry, neurodegeneration, metabolic and inflammatory disorders. Drugs that target the proteins controlling chromatin modifications can modulate the expression of clusters of genes, potentially offering higher therapeutic efficacy than classical agents with single target pharmacologies that are susceptible to biochemical pathway degeneracy. Here, we summarize recent research linking epigenetic dysregulation with diseases in neurosciences, the application of relevant animal models, and the potential for small molecule modulator development to facilitate target discovery, validation and translation into clinical treatments.
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Affiliation(s)
- Chas Bountra
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ, UK,
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Niesen FH, Schultz L, Jadhav A, Bhatia C, Guo K, Maloney DJ, Pilka ES, Wang M, Oppermann U, Heightman TD, Simeonov A. High-affinity inhibitors of human NAD-dependent 15-hydroxyprostaglandin dehydrogenase: mechanisms of inhibition and structure-activity relationships. PLoS One 2010; 5:e13719. [PMID: 21072165 PMCID: PMC2970562 DOI: 10.1371/journal.pone.0013719] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 10/04/2010] [Indexed: 12/12/2022] Open
Abstract
Background 15-hydroxyprostaglandin dehydrogenase (15-PGDH, EC 1.1.1.141) is the key enzyme for the inactivation of prostaglandins, regulating processes such as inflammation or proliferation. The anabolic pathways of prostaglandins, especially with respect to regulation of the cyclooxygenase (COX) enzymes have been studied in detail; however, little is known about downstream events including functional interaction of prostaglandin-processing and -metabolizing enzymes. High-affinity probes for 15-PGDH will, therefore, represent important tools for further studies. Principal Findings To identify novel high-affinity inhibitors of 15-PGDH we performed a quantitative high-throughput screen (qHTS) by testing >160 thousand compounds in a concentration-response format and identified compounds that act as noncompetitive inhibitors as well as a competitive inhibitor, with nanomolar affinity. Both types of inhibitors caused strong thermal stabilization of the enzyme, with cofactor dependencies correlating with their mechanism of action. We solved the structure of human 15-PGDH and explored the binding modes of the inhibitors to the enzyme in silico. We found binding modes that are consistent with the observed mechanisms of action. Conclusions Low cross-reactivity in screens of over 320 targets, including three other human dehydrogenases/reductases, suggest selectivity of the present inhibitors for 15-PGDH. The high potencies and different mechanisms of action of these chemotypes make them a useful set of complementary chemical probes for functional studies of prostaglandin-signaling pathways. Enhanced version This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S2.
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Affiliation(s)
- Frank H. Niesen
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Lena Schultz
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ajit Jadhav
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chitra Bhatia
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Kunde Guo
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - David J. Maloney
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ewa S. Pilka
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Minghua Wang
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Udo Oppermann
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Biomedical Research Unit, Nuffield Department of Orthopedic Surgery, Rheumatology and Musculoskeletal Sciences, Botnar Research Center, University of Oxford, Oxford, United Kingdom
| | - Tom D. Heightman
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Anton Simeonov
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Bailey JM, Scott JS, Basilla JB, Bolton VJ, Boyfield I, Evans DG, Fleury E, Heightman TD, Jarvie EM, Lawless K, Matthews KL, McKay F, Mok H, Muir A, Orlek BS, Sanger GJ, Stemp G, Stevens AJ, Thompson M, Ward J, Vaidya K, Westaway SM. The discovery and optimisation of benzazepine sulfonamide and sulfones as potent agonists of the motilin receptor. Bioorg Med Chem Lett 2009; 19:6452-8. [DOI: 10.1016/j.bmcl.2009.09.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Revised: 09/04/2009] [Accepted: 09/05/2009] [Indexed: 10/20/2022]
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Abstract
Holocarboxylase synthetase (HCS, eukaryotic enzyme) and BirA (prokaryotic) are biotin protein ligases that catalyze the ATP-dependent attachment of biotin to apocarboxylases via the reactive intermediate, bio-5'-AMP. In this study, we examined the in vitro mechanism of biotin attachment to histone H2A in the presence of HCS and BirA. The experiment derives from our observations that HCS is found in the nucleus of cells in addition to the cytoplasm, and it has the ability to attach biotin to histones in vitro (Narang et al., Hum Mol Genet 2004; 13:15-23). Using recombinant HCS or BirA, the rate of biotin attachment was considerably slower with histone H2A than with the biotin binding domain of an apocarboxylase. However, on incubation of recombinant H2A with chemically synthesized bio-5'-AMP, H2A was observed to be rapidly labeled with biotin in the absence of enzyme. Nonenzymatic biotinylation of a truncated apocarboxylase (BCCP87) has been previously reported (Streaker and Beckett, Protein Sci 2006; 15:1928-1935), though at a much slower rate than we observe for H2A. The specific attachment sites of nonenzymatically biotinylated recombinant H2A at different time points were identified using mass spectrometry, and were found to consist of a similar pattern of biotin attachment as seen in the presence of HCS, with preference for lysines in the highly basic N-terminal region of the histone. None of the lysine sites within H2A resembles the biotin attachment consensus sequence seen in carboxylases, suggesting a novel mechanism for histone biotinylation.
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Affiliation(s)
- Shannon Healy
- Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada.
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46
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Witherington J, Abberley L, Bellenie BR, Boatman R, Collis K, Dean DK, Gaiba A, Paul King N, Shuker N, Steadman JG, Takle AK, Sanger G, Butler S, McKay F, Muir A, Winborn K, Ward RW, Heightman TD. Aryl sulphonyl amides as potent agonists of the growth hormone secretagogue (ghrelin) receptor. Bioorg Med Chem Lett 2009; 19:684-7. [DOI: 10.1016/j.bmcl.2008.12.042] [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: 11/13/2008] [Revised: 12/09/2008] [Accepted: 12/09/2008] [Indexed: 12/26/2022]
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47
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Westaway SM, Brown SL, Conway E, Heightman TD, Johnson CN, Lapsley K, Macdonald GJ, MacPherson DT, Mitchell DJ, Myatt JW, Seal JT, Stanway SJ, Stemp G, Thompson M, Celestini P, Colombo A, Consonni A, Gagliardi S, Riccaboni M, Ronzoni S, Briggs MA, Matthews KL, Stevens AJ, Bolton VJ, Boyfield I, Jarvie EM, Stratton SC, Sanger GJ. The discovery of biaryl carboxamides as novel small molecule agonists of the motilin receptor. Bioorg Med Chem Lett 2008; 18:6429-36. [DOI: 10.1016/j.bmcl.2008.10.072] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Revised: 10/15/2008] [Accepted: 10/16/2008] [Indexed: 11/26/2022]
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48
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Heightman TD, Conway E, Corbett DF, Macdonald GJ, Stemp G, Westaway SM, Celestini P, Gagliardi S, Riccaboni M, Ronzoni S, Vaidya K, Butler S, McKay F, Muir A, Powney B, Winborn K, Wise A, Jarvie EM, Sanger GJ. Identification of small molecule agonists of the motilin receptor. Bioorg Med Chem Lett 2008; 18:6423-8. [PMID: 18980843 DOI: 10.1016/j.bmcl.2008.10.071] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Revised: 10/15/2008] [Accepted: 10/16/2008] [Indexed: 11/19/2022]
Abstract
High-throughput screening resulted in the identification of a series of novel motilin receptor agonists with relatively low molecular weights. The series originated from an array of biphenyl derivatives designed to target 7-transmembrane (7-TM) receptors. Further investigation of the structure-activity relationship within the series resulted in the identification of compound (22) as a potent and selective agonist at the motilin receptor.
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Affiliation(s)
- Tom D Heightman
- Neurology & GI Centre of Excellence for Drug Discovery, GlaxoSmithKline, New Frontiers Science Park, Third Avenue, Harlow, Essex CM19 5AW, UK.
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49
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Hodgson DM, Hughes SP, Thompson AL, Heightman TD. Terminal aziridines by alpha-deprotonation/electrophile trapping of N-protected aziridine. Org Lett 2008; 10:3453-6. [PMID: 18613698 DOI: 10.1021/ol801224g] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
N-tert-Butylsulfonyl and N-tert-butylsulfinyl aziridine undergo alpha-lithiation/electrophile trapping providing a new entry to terminal aziridines. With N-tert-butylsulfinyl aziridine complete asymmetric induction is observed alpha to nitrogen.
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Affiliation(s)
- David M Hodgson
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK.
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50
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Witherington J, Abberley L, Briggs MA, Collis K, Dean DK, Gaiba A, King NP, Kraus H, Shuker N, Steadman JG, Takle AK, Sanger G, Wadsworth G, Butler S, McKay F, Muir A, Winborn K, Heightman TD. Potent achiral agonists of the growth hormone secretagogue (ghrelin) receptor. Part 2: Lead optimisation. Bioorg Med Chem Lett 2008; 18:2203-5. [DOI: 10.1016/j.bmcl.2007.12.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Revised: 12/10/2007] [Accepted: 12/11/2007] [Indexed: 12/26/2022]
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