1
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Day JEH, Berdini V, Castro J, Chessari G, Davies TG, Day PJ, St Denis JD, Fujiwara H, Fukaya S, Hamlett CCF, Hearn K, Hiscock SD, Holvey RS, Ito S, Kandola N, Kodama Y, Liebeschuetz JW, Martins V, Matsuo K, Mortenson PN, Muench S, Nakatsuru Y, Ochiiwa H, Palmer N, Peakman T, Price A, Reader M, Rees DC, Rich SJ, Shah A, Shibata Y, Smyth T, Twigg DG, Wallis NG, Williams G, Wilsher NE, Woodhead A, Shimamura T, Johnson CN. Fragment-Based Discovery of Allosteric Inhibitors of SH2 Domain-Containing Protein Tyrosine Phosphatase-2 (SHP2). J Med Chem 2024. [PMID: 38462716 DOI: 10.1021/acs.jmedchem.3c02118] [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: 03/12/2024]
Abstract
The ubiquitously expressed protein tyrosine phosphatase SHP2 is required for signaling downstream of receptor tyrosine kinases (RTKs) and plays a role in regulating many cellular processes. Genetic knockdown and pharmacological inhibition of SHP2 suppresses RAS/MAPK signaling and inhibit the proliferation of RTK-driven cancer cell lines. Here, we describe the first reported fragment-to-lead campaign against SHP2, where X-ray crystallography and biophysical techniques were used to identify fragments binding to multiple sites on SHP2. Structure-guided optimization, including several computational methods, led to the discovery of two structurally distinct series of SHP2 inhibitors binding to the previously reported allosteric tunnel binding site (Tunnel Site). One of these series was advanced to a low-nanomolar lead that inhibited tumor growth when dosed orally to mice bearing HCC827 xenografts. Furthermore, a third series of SHP2 inhibitors was discovered binding to a previously unreported site, lying at the interface of the C-terminal SH2 and catalytic domains.
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Affiliation(s)
- James E H Day
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Valerio Berdini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Joan Castro
- 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
| | - Thomas G Davies
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Philip J Day
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Jeffrey D St Denis
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Hideto Fujiwara
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Satoshi Fukaya
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | | | - Keisha Hearn
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Steven D Hiscock
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Rhian S Holvey
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Satoru Ito
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Navrohit Kandola
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Yasuo Kodama
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - John W Liebeschuetz
- 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
| | - Kenichi Matsuo
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Paul N Mortenson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Sandra Muench
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Yoko Nakatsuru
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Hiroaki Ochiiwa
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Nicholas Palmer
- 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
| | - Amanda Price
- 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
| | - David C Rees
- 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
| | - Alpesh Shah
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Yoshihiro Shibata
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Tomoko Smyth
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - David G Twigg
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Nicola G Wallis
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Glyn 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
| | - Andrew Woodhead
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Tadashi Shimamura
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Christopher N Johnson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
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2
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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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3
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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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4
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Munck J, Berdini V, Courtin A, East C, Heightman T, Hindley C, Kucia-Tran J, Lyons J, Martins V, Muench S, Murray C, Norton D, O’Reilly M, Reader M, Rees D, Rich S, Thompson N, Wilsher N, Woolford A, Wallis N. The clinical candidate, ASTX029, is a novel, dual mechanism ERK1/2 inhibitor and has potent activity in MAPK-activated cancer cell lines and in vivo tumor models. Eur J Cancer 2020. [DOI: 10.1016/s0959-8049(20)31218-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5
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Hearn K, Berdini V, Chessari G, Davies T, Day J, Hamlett C, Hiscock S, Martins V, Muench S, Nakatsuru Y, Ochiiwa H, Price A, Rich S, Shah A, Shibata Y, Shimamura T, Smyth T, Wallis N, Wilsher N, Johnson C. Identification of potent small molecule allosteric inhibitors of SHP2. Eur J Cancer 2020. [DOI: 10.1016/s0959-8049(20)31193-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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Day PJ, Berdini V, Castro J, Chessari G, Davies TG, Day JE, Fukaya S, Hamlett C, Hearn K, Hiscock S, Holvey R, Ito S, Kodama Y, Matsuo K, Nakatsuru Y, Palmer N, Price A, Shimamura T, Denis JD, Wallis NG, Williams G, Johnson CN. Abstract 1039: Fragment-based drug discovery to identify small molecule allosteric inhibitors of SHP2. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1039] [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 ubiquitously expressed protein tyrosine phosphatase SHP2 is required for signalling downstream of receptor tyrosine kinases (RTKs) and plays a role in regulating many cellular processes. Recent advances have shown that genetic knockdown and pharmacological inhibition of SHP2 suppresses RAS/MAPK signalling and inhibits proliferation of RTK-driven cancer cell lines. SHP2 is now understood to act upstream of RAS and plays a role in KRAS-driven cancers, an area of research which is rapidly growing. Considering that RTK deregulation often leads to a wide range of cancers and the newly appreciated role of SHP2 in KRAS-driven cancers, SHP2 inhibitors are therefore a promising therapeutic approach.
SHP2 contains two N-terminal tandem SH2 domains (N-SH2, C-SH2), a catalytic phosphatase domain and a C-terminal tail. SHP2 switches between “open” active and “closed” inactive forms due to autoinhibitory interactions between the N-SH2 domain and the phosphatase domain. Historically, phosphatases were deemed undruggable as there had been no advancements with active site inhibitors. We hypothesised that fragment screening would be highly applicable and amenable to this target to enable alternative means of inhibition through identification of allosteric binding sites. Here we describe the first reported fragment screen against SHP2.
Using our fragment-based PyramidTM approach, screening was carried out on two constructs of SHP2; a closed autoinhibited C-terminal truncated form (phosphatase and both SH2 domains), as well as the phosphatase-only domain. A combination of screening methods such as X-ray crystallography and NMR were employed to identify fragment hits at multiple sites on SHP2, including the tunnel-like allosteric site reported by Chen et al, 2016. Initial fragment hits had affinities for SHP2 in the range of 1mM as measured by ITC. Binding of these hits was improved using structure-guided design to generate compounds which inhibit SHP2 phosphatase activity and are promising starting points for further optimization.
Citation Format: Philip J. Day, Valerio Berdini, Juan Castro, Gianni Chessari, Thomas G. Davies, James E. Day, Satoshi Fukaya, Chris Hamlett, Keisha Hearn, Steve Hiscock, Rhian Holvey, Satoru Ito, Yasuo Kodama, Kenichi Matsuo, Yoko Nakatsuru, Nick Palmer, Amanda Price, Tadashi Shimamura, Jeffrey D.St. Denis, Nicola G. Wallis, Glyn Williams, Christopher N. Johnson. Fragment-based drug discovery to identify small molecule allosteric inhibitors of SHP2 [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1039.
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Affiliation(s)
- Philip J. Day
- 1Astex Pharmaceuticals, Inc., Cambridge, United Kingdom
| | | | - Juan Castro
- 1Astex Pharmaceuticals, Inc., Cambridge, United Kingdom
| | | | | | - James E. Day
- 1Astex Pharmaceuticals, Inc., Cambridge, United Kingdom
| | | | - Chris Hamlett
- 1Astex Pharmaceuticals, Inc., Cambridge, United Kingdom
| | - Keisha Hearn
- 1Astex Pharmaceuticals, Inc., Cambridge, United Kingdom
| | - Steve Hiscock
- 1Astex Pharmaceuticals, Inc., Cambridge, United Kingdom
| | - Rhian Holvey
- 1Astex Pharmaceuticals, Inc., Cambridge, United Kingdom
| | - Satoru Ito
- 2Taiho Pharmaceutical Co., Ltd, Tsukuba, Japan
| | | | | | | | - Nick Palmer
- 1Astex Pharmaceuticals, Inc., Cambridge, United Kingdom
| | - Amanda Price
- 1Astex Pharmaceuticals, Inc., Cambridge, United Kingdom
| | | | | | | | - Glyn Williams
- 1Astex Pharmaceuticals, Inc., Cambridge, United Kingdom
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7
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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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8
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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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9
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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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10
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Woolford AJA, Day PJ, Bénéton V, Berdini V, Coyle JE, Dudit Y, Grondin P, Huet P, Lee LYW, Manas ES, McMenamin RL, Murray CW, Page LW, Patel VK, Potvain F, Rich SJ, Sang Y, Somers DO, Trottet L, Wan Z, Zhang X. Fragment-Based Approach to the Development of an Orally Bioavailable Lactam Inhibitor of Lipoprotein-Associated Phospholipase A2 (Lp-PLA2). J Med Chem 2016; 59:10738-10749. [DOI: 10.1021/acs.jmedchem.6b01427] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Alison J.-A. Woolford
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Philip J. Day
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Véronique Bénéton
- Centre
de Recherches Francois Hyafil, GlaxoSmithKline, 25−27 Avenue du Québec, Les Ulis, France
| | - Valerio Berdini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Joseph E. Coyle
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Yann Dudit
- Centre
de Recherches Francois Hyafil, GlaxoSmithKline, 25−27 Avenue du Québec, Les Ulis, France
| | - Pascal Grondin
- Centre
de Recherches Francois Hyafil, GlaxoSmithKline, 25−27 Avenue du Québec, Les Ulis, France
| | - Pascal Huet
- Centre
de Recherches Francois Hyafil, GlaxoSmithKline, 25−27 Avenue du Québec, Les Ulis, France
| | - Lydia Y. W. Lee
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Eric S. Manas
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Rachel L. McMenamin
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Christopher W. Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Lee W. Page
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | | | - Florent Potvain
- Centre
de Recherches Francois Hyafil, GlaxoSmithKline, 25−27 Avenue du Québec, Les Ulis, France
| | - Sharna J. Rich
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Yingxia Sang
- Neurodegeneration
DPU, GlaxoSmithKline, 898 Halei Road, Zhangjiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Don O. Somers
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, United Kingdom
| | - Lionel Trottet
- Centre
de Recherches Francois Hyafil, GlaxoSmithKline, 25−27 Avenue du Québec, Les Ulis, France
| | - Zehong Wan
- Neurodegeneration
DPU, GlaxoSmithKline, 898 Halei Road, Zhangjiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Xiaomin Zhang
- Neurodegeneration
DPU, GlaxoSmithKline, 898 Halei Road, Zhangjiang Hi-Tech
Park, Pudong, Shanghai 201203, China
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11
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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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12
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Woolford AJA, Pero JE, Aravapalli S, Berdini V, Coyle JE, Day PJ, Dodson AM, Grondin P, Holding FP, Lee LYW, Li P, Manas ES, Marino J, Martin ACL, McCleland BW, McMenamin RL, Murray CW, Neipp CE, Page LW, Patel VK, Potvain F, Rich S, Rivero RA, Smith K, Somers DO, Trottet L, Velagaleti R, Williams G, Xie R. Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Discovered through X-ray Fragment Screening. J Med Chem 2016; 59:5356-67. [DOI: 10.1021/acs.jmedchem.6b00212] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Alison J.-A. Woolford
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Joseph E. Pero
- GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Sridhar Aravapalli
- GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Valerio Berdini
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Joseph E. Coyle
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Philip J. Day
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Andrew M. Dodson
- GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Pascal Grondin
- Centre
de Recherches Francois Hyafil, GlaxoSmithKline, 25-27 Avenue du Québec, Les Ulis, France
| | - Finn P. Holding
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Lydia Y. W. Lee
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Peng Li
- GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Eric S. Manas
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Joseph Marino
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Agnes C. L. Martin
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Brent W. McCleland
- GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Rachel L. McMenamin
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Christopher W. Murray
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Christopher E. Neipp
- GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Lee W. Page
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | | | - Florent Potvain
- Centre
de Recherches Francois Hyafil, GlaxoSmithKline, 25-27 Avenue du Québec, Les Ulis, France
| | - Sharna Rich
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Ralph A. Rivero
- GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Kirsten Smith
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Donald O. Somers
- GlaxoSmithKline, Gunnels
Wood Road, Stevenage SG1
2NY, United Kingdom
| | - Lionel Trottet
- Centre
de Recherches Francois Hyafil, GlaxoSmithKline, 25-27 Avenue du Québec, Les Ulis, France
| | - Ranganadh Velagaleti
- GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Glyn Williams
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Ren Xie
- GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
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13
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Pathuri P, Saalau-Bethell SM, Woodhead AJ, Berdini V, Carr MG, Chessari G, Cleasby A, Congreve M, Coyle JE, Graham B, Hiscock SD, Lock V, Murray CW, O'Brien MA, Rich SJ, Richardson CJ, Sambrook T, Vinkovic M, Williams PA, Yon JR, Jhoti H. Identification of novel allosteric inhibitors through fragment-based drug discovery and X-ray crystallography. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315099398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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14
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Murray CW, Berdini V, Buck IM, Carr ME, Cleasby A, Coyle JE, Curry JE, Day JEH, Day PJ, Hearn K, Iqbal A, Lee LYW, Martins V, Mortenson PN, Munck JM, Page LW, Patel S, Roomans S, Smith K, Tamanini E, Saxty G. Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors. ACS Med Chem Lett 2015; 6:798-803. [PMID: 26191369 DOI: 10.1021/acsmedchemlett.5b00143] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [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: 04/07/2015] [Accepted: 06/04/2015] [Indexed: 12/24/2022] Open
Abstract
The DDR1 and DDR2 receptor tyrosine kinases are activated by extracellular collagen and have been implicated in a number of human diseases including cancer. We performed a fragment-based screen against DDR1 and identified fragments that bound either at the hinge or in the back pocket associated with the DFG-out conformation of the kinase. Modeling based on crystal structures of potent kinase inhibitors facilitated the "back-to-front" design of potent DDR1/2 inhibitors that incorporated one of the DFG-out fragments. Further optimization led to low nanomolar, orally bioavailable inhibitors that were selective for DDR1 and DDR2. The inhibitors were shown to potently inhibit DDR2 activity in cells but in contrast to unselective inhibitors such as dasatinib, they did not inhibit proliferation of mutant DDR2 lung SCC cell lines.
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Affiliation(s)
- Christopher W. Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Valerio Berdini
- 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
| | - Maria E. Carr
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Anne Cleasby
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Joseph E. Coyle
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Jayne E. Curry
- 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
| | - Phillip J. Day
- 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
| | - Aman Iqbal
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Lydia Y. W. Lee
- 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
| | - Paul N. Mortenson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Joanne M. Munck
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Lee W. Page
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Sahil Patel
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Susan Roomans
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Kirsten Smith
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Emiliano Tamanini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Gordon Saxty
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
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15
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Johnson CN, Adelinet C, Berdini V, Beke L, Bonnet P, Brehmer D, Calo F, Coyle JE, Day PJ, Frederickson M, Freyne EJE, Gilissen RAHJ, Hamlett CCF, Howard S, Meerpoel L, Mevellec L, McMenamin R, Pasquier E, Patel S, Rees DC, Linders JTM. Structure-Based Design of Type II Inhibitors Applied to Maternal Embryonic Leucine Zipper Kinase. ACS Med Chem Lett 2015; 6:31-6. [PMID: 25589926 DOI: 10.1021/ml5001273] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [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: 03/28/2014] [Accepted: 05/15/2014] [Indexed: 11/28/2022] Open
Abstract
A novel Type II kinase inhibitor chemotype has been identified for maternal embryonic leucine zipper kinase (MELK) using structure-based ligand design. The strategy involved structural characterization of an induced DFG-out pocket by protein-ligand X-ray crystallography and incorporation of a slender linkage capable of bypassing a large gate-keeper residue, thus enabling design of molecules accessing both hinge and induced pocket regions. Optimization of an initial hit led to the identification of a low-nanomolar, cell-penetrant Type II inhibitor suitable for use as a chemical probe for MELK.
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Affiliation(s)
- Christopher N. Johnson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Christophe Adelinet
- Janssen Research and Development, A Division of Janssen-Cilag , BP615-Chaussée
du Vexin, 27106 Val-de-Reuil, France
| | - Valerio Berdini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Lijs Beke
- Janssen Research and Development, A Division of Janssen Pharmaceutica N.V., Turnhoutseweg 30, Beerse 2340, Belgium
| | - Pascal Bonnet
- Janssen Research and Development, A Division of Janssen Pharmaceutica N.V., Turnhoutseweg 30, Beerse 2340, Belgium
| | - Dirk Brehmer
- Janssen Research and Development, A Division of Janssen Pharmaceutica N.V., Turnhoutseweg 30, Beerse 2340, Belgium
| | - Frederick Calo
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Joseph E. Coyle
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Phillip J. Day
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Martyn Frederickson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Eddy J. E. Freyne
- Janssen Research and Development, A Division of Janssen Pharmaceutica N.V., Turnhoutseweg 30, Beerse 2340, Belgium
| | - Ron A. H. J. Gilissen
- Janssen Research and Development, A Division of Janssen Pharmaceutica N.V., Turnhoutseweg 30, Beerse 2340, Belgium
| | | | - Steven Howard
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Lieven Meerpoel
- Janssen Research and Development, A Division of Janssen Pharmaceutica N.V., Turnhoutseweg 30, Beerse 2340, Belgium
| | - Laurence Mevellec
- Janssen Research and Development, A Division of Janssen-Cilag , BP615-Chaussée
du Vexin, 27106 Val-de-Reuil, France
| | - Rachel McMenamin
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Elisabeth Pasquier
- Janssen Research and Development, A Division of Janssen-Cilag , BP615-Chaussée
du Vexin, 27106 Val-de-Reuil, France
| | - Sahil Patel
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - David C. Rees
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Joannes T. M. Linders
- Janssen Research and Development, A Division of Janssen Pharmaceutica N.V., Turnhoutseweg 30, Beerse 2340, Belgium
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16
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Johnson CN, Berdini V, Beke L, Bonnet P, Brehmer D, Coyle JE, Day PJ, Frederickson M, Freyne EJE, Gilissen RAHJ, Hamlett CCF, Howard S, Meerpoel L, McMenamin R, Patel S, Rees DC, Sharff A, Sommen F, Wu T, Linders JTM. Fragment-based discovery of type I inhibitors of maternal embryonic leucine zipper kinase. ACS Med Chem Lett 2015; 6:25-30. [PMID: 25589925 DOI: 10.1021/ml5001245] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [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: 03/27/2014] [Accepted: 05/15/2014] [Indexed: 11/30/2022] Open
Abstract
Fragment-based drug design was successfully applied to maternal embryonic leucine zipper kinase (MELK). A low affinity (160 μM) fragment hit was identified, which bound to the hinge region with an atypical binding mode, and this was optimized using structure-based design into a low-nanomolar and cell-penetrant inhibitor, with a good selectivity profile, suitable for use as a chemical probe for elucidation of MELK biology.
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Affiliation(s)
- Christopher N. Johnson
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Valerio Berdini
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Lijs Beke
- Janssen Research and Development, A Division of Janssen Pharmaceutica N.V., Turnhoutseweg 30, Beerse 2340 Belgium
| | - Pascal Bonnet
- Janssen Research and Development, A Division of Janssen Pharmaceutica N.V., Turnhoutseweg 30, Beerse 2340 Belgium
| | - Dirk Brehmer
- Janssen Research and Development, A Division of Janssen Pharmaceutica N.V., Turnhoutseweg 30, Beerse 2340 Belgium
| | - Joseph E. Coyle
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Phillip J. Day
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Martyn Frederickson
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Eddy J. E. Freyne
- Janssen Research and Development, A Division of Janssen Pharmaceutica N.V., Turnhoutseweg 30, Beerse 2340 Belgium
| | - Ron A. H. J. Gilissen
- Janssen Research and Development, A Division of Janssen Pharmaceutica N.V., Turnhoutseweg 30, Beerse 2340 Belgium
| | | | - Steven Howard
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Lieven Meerpoel
- Janssen Research and Development, A Division of Janssen Pharmaceutica N.V., Turnhoutseweg 30, Beerse 2340 Belgium
| | - Rachel McMenamin
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Sahil Patel
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - David C. Rees
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Andrew Sharff
- Astex Pharmaceuticals, 436
Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - François Sommen
- Janssen Research and Development, A Division of Janssen Pharmaceutica N.V., Turnhoutseweg 30, Beerse 2340 Belgium
| | - Tongfei Wu
- Janssen Research and Development, A Division of Janssen Pharmaceutica N.V., Turnhoutseweg 30, Beerse 2340 Belgium
| | - Joannes T. M. Linders
- Janssen Research and Development, A Division of Janssen Pharmaceutica N.V., Turnhoutseweg 30, Beerse 2340 Belgium
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17
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Angibaud P, Querolle O, Berdini V, Saxty G, Cleasby A, Colombel H, Csoka I, Esser N, Gilissen R, Meerpoel L, Paulussen C, Pilatte I, Poncelet V, Rees D, Roux B, Verhulst T, Tronel V, Wroblowski B, Murray C, Vialard J. 400 Optimization of novel pyrido[2,3-b]pyrazine based small molecule fibroblast growth factor receptor 1, 2, 3 & 4 (FGFR) inhibitors into a potential clinical candidate. Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)70526-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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18
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Saalau-Bethell SM, Berdini V, Cleasby A, Congreve M, Coyle JE, Lock V, Murray CW, O'Brien MA, Rich SJ, Sambrook T, Vinkovic M, Yon JR, Jhoti H. Crystal structure of human soluble adenylate cyclase reveals a distinct, highly flexible allosteric bicarbonate binding pocket. ChemMedChem 2014; 9:823-32. [PMID: 24616449 PMCID: PMC4506562 DOI: 10.1002/cmdc.201300480] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [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: 11/25/2013] [Indexed: 11/25/2022]
Abstract
Soluble adenylate cyclases catalyse the synthesis of the second messenger cAMP through the cyclisation of ATP and are the only known enzymes to be directly activated by bicarbonate. Here, we report the first crystal structure of the human enzyme that reveals a pseudosymmetrical arrangement of two catalytic domains to produce a single competent active site and a novel discrete bicarbonate binding pocket. Crystal structures of the apo protein, the protein in complex with α,β-methylene adenosine 5′-triphosphate (AMPCPP) and calcium, with the allosteric activator bicarbonate, and also with a number of inhibitors identified using fragment screening, all show a flexible active site that undergoes significant conformational changes on binding of ligands. The resulting nanomolar-potent inhibitors that were developed bind at both the substrate binding pocket and the allosteric site, and can be used as chemical probes to further elucidate the function of this protein.
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19
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Abstract
Protein kinases are one of the most important families of drug targets, and aberrant kinase activity has been linked to a large number of disease areas. Although eminently targetable using small molecules, kinases present a number of challenges as drug targets, not least obtaining selectivity across such a large and relatively closely related target family. Fragment-based drug discovery involves screening simple, low-molecular weight compounds to generate initial hits against a target. These hits are then optimized to more potent compounds via medicinal chemistry, usually facilitated by structural biology. Here, we will present a number of recent examples of fragment-based approaches to the discovery of kinase inhibitors, detailing the construction of fragment-screening libraries, the identification and validation of fragment hits, and their optimization into potent and selective lead compounds. The advantages of fragment-based methodologies will be discussed, along with some of the challenges associated with using this route. Finally, we will present a number of key lessons derived both from our own experience running fragment screens against kinases and from a large number of published studies.
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20
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Smyth T, Curry J, Wilsher N, Johnson C, Berdini V, Richardson C, Massey F, McMenamin R, Griffiths-Jones C, Thompson N, Wallis NG. Abstract 2315: Pharmacodynamic and antitumor activity of fragment-derived inhibitors of MetAP2 in tumor xenografts. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-2315] [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
Background: Methionine aminopeptidase (MetAP) 2 is one of the two eukaryotic enzymes responsible for cleaving the N-terminal methionine from newly synthesized polypeptides to allow further post-translational modifications such as myristoylation to take place. The enzyme is the target of the anti-angiogenic natural product, fumagillin and so is believed to play a role in angiogenesis. Fumagillin analogues have shown activity in several disease models including oncology, inflammation and obesity indicating MetAP2 is a promising target in a number of indications. The semi-synthetic fumagillin analogue, TNP470, has shown activity in a Phase I/II cancer trial, suggesting that MetAP2 is a good oncology target. Here we describe the discovery, optimization and anti-tumor activity of fragment-derived MetAP2 inhibitors. Results: We identified fragment hits to MetAP2 using our fragment-based screening approach, Pyramid™. These were optimized by structure-based drug design to novel, potent lead compounds with sub-100 nM potency against the isolated MetAP2 enzyme. The two most advanced compounds inhibited proliferation of HUVECs with potencies of 130 nM and 300 nM. Levels of the MetAP2 substrate, Met-14-3-3, were shown to increase on treatment of HUVECs with these compounds indicating that Met-14-3-3 was not being processed and hence MetAP2 was being inhibited. The compounds also inhibited HUVEC tubule formation demonstrating their anti-angiogenic properties. The two lead compounds were further tested in vivo. Both compounds were well tolerated at doses up to 200 mg/kg bid. Levels of Met-14-3-3 were seen to increase in the thymus and spleen (where high expression of MetAP2 has been reported) of mice treated with the compounds, indicating again that MetAP2 was being inhibited in these tissues. Compound 1 was tested in a mouse HCT116 xenograft model. Mice were subcutaneously inoculated with HCT116 cells and oral dosing at 200 mg/kg bid started one day later. Tumor growth was inhibited in treated mice compared with control and growth inhibition was greater in Compound 1 treated mice (T/C 46%) compared with mice treated with 30 mg/kg TNP470 subcutaneously q2d (T/C 61%). Conclusions: The compounds described here are novel small-molecule inhibitors of MetAP2. Their promising tumor growth inhibitory properties merit their testing in further tumor models and potentially other indications.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2315. doi:1538-7445.AM2012-2315
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Affiliation(s)
- Tomoko Smyth
- 1Astex Pharmaceuticals Inc, Cambridge, United Kingdom
| | - Jayne Curry
- 1Astex Pharmaceuticals Inc, Cambridge, United Kingdom
| | | | - Chris Johnson
- 1Astex Pharmaceuticals Inc, Cambridge, United Kingdom
| | | | | | | | | | | | - Neil Thompson
- 1Astex Pharmaceuticals Inc, Cambridge, United Kingdom
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21
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Squires M, Ward G, Saxty G, Berdini V, Cleasby A, King P, Angibaud P, Perera T, Fazal L, Ross D, Jones CG, Madin A, Benning RK, Vickerstaffe E, O'Brien A, Frederickson M, Reader M, Hamlett C, Batey MA, Rich S, Carr M, Miller D, Feltell R, Thiru A, Bethell S, Devine LA, Graham BL, Pike A, Cosme J, Lewis EJ, Freyne E, Lyons J, Irving J, Murray C, Newell DR, Thompson NT. Potent, selective inhibitors of fibroblast growth factor receptor define fibroblast growth factor dependence in preclinical cancer models. Mol Cancer Ther 2011; 10:1542-52. [PMID: 21764904 DOI: 10.1158/1535-7163.mct-11-0426] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We describe here the identification and characterization of 2 novel inhibitors of the fibroblast growth factor receptor (FGFR) family of receptor tyrosine kinases. The compounds exhibit selective inhibition of FGFR over the closely related VEGFR2 receptor in cell lines and in vivo. The pharmacologic profile of these inhibitors was defined using a panel of human tumor cell lines characterized for specific mutations, amplifications, or translocations known to activate one of the four FGFR receptor isoforms. This pharmacology defines a profile for inhibitors that are likely to be of use in clinical settings in disease types where FGFR is shown to play an important role.
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22
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Saxty G, Akkari R, Angibaud P, Arts J, Benderitter P, Berdini V, Bonnet P, Cleasby A, Embrechts W, Freyne E, Gilissen R, King P, Lacrampe J, Ligny Y, Madin A, Mcclue S, Mevellec L, Murray CW, Newell H, Page M, Papanikos A, Perera T, Querolle O, Rees DC, Rich SJ, Saalau-Bethell SM, Sement E, Simmonet Y, Squires M, Tronel V, Ward GA, Willems M, B W, Thompson NT. Abstract 1361: Fragment based drug discovery of selective inhibitors of Fibroblast Growth Factor Receptor (FGFR). Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-1361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent data in a number of tumour types has implicated Fibroblast Growth Factor (FGF) and Fibroblast Growth Factor receptor (FGFR) signalling as being key to the molecular pathology of cancer.
A fragment screening campaign was conducted against the tyrosine kinase domain of FGFR1 to detect low molecular weight compounds that bound to the hinge region of the kinase. The screening produced several fragment inhibitors (molecular weight <250 Da) in the micromolar range and their binding modes were confirmed by X-ray crystallography. We selected an imidazo[1,2-a]pyridine fragment that was 120 uM versus FGFR3 in the kinase inhibition bioassay. Subsequently, in the fragments-to-leads stage a detailed structural understanding of the binding interactions between the fragment and its protein kinase target, using X-ray crystallography, led to the identification of a 0.003 uM inhibitor of FGFR3 in the kinase bioassay, with significant selectivity versus VEGFR2 and FLT3.
The poster will focus on the description of previously undescribed compounds bearing an imidazo[1,2-a]pyridine core scaffold where selectivity versus other protein kinases, for example FLT3, is obtained using the X-ray crystal structure and structure-based design. In summary we will illustrate how X-ray crystallography and fragment-based drug design (FBDD) can be used to discover compounds with activity in an FGFR driven xenograft model when dosed by the oral route.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1361. doi:10.1158/1538-7445.AM2011-1361
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Affiliation(s)
| | - R Akkari
- 2Janssen Oncology R&D, Beerse, Belgium
| | | | - J Arts
- 2Janssen Oncology R&D, Beerse, Belgium
| | | | - V Berdini
- 1Astex Therapeutics, Cambridge, United Kingdom
| | - P Bonnet
- 2Janssen Oncology R&D, Beerse, Belgium
| | - A Cleasby
- 1Astex Therapeutics, Cambridge, United Kingdom
| | | | - E Freyne
- 2Janssen Oncology R&D, Beerse, Belgium
| | | | - P King
- 2Janssen Oncology R&D, Beerse, Belgium
| | | | - Y Ligny
- 2Janssen Oncology R&D, Beerse, Belgium
| | - A Madin
- 1Astex Therapeutics, Cambridge, United Kingdom
| | - S Mcclue
- 2Janssen Oncology R&D, Beerse, Belgium
| | | | - C W. Murray
- 1Astex Therapeutics, Cambridge, United Kingdom
| | - H Newell
- 3Northern Institute for Cancer Research, Newcastle, United Kingdom
| | - M Page
- 2Janssen Oncology R&D, Beerse, Belgium
| | | | - T Perera
- 2Janssen Oncology R&D, Beerse, Belgium
| | | | - D C. Rees
- 1Astex Therapeutics, Cambridge, United Kingdom
| | - S J. Rich
- 1Astex Therapeutics, Cambridge, United Kingdom
| | | | - E Sement
- 2Janssen Oncology R&D, Beerse, Belgium
| | | | - M Squires
- 1Astex Therapeutics, Cambridge, United Kingdom
| | - V Tronel
- 2Janssen Oncology R&D, Beerse, Belgium
| | - G A. Ward
- 1Astex Therapeutics, Cambridge, United Kingdom
| | - M Willems
- 2Janssen Oncology R&D, Beerse, Belgium
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23
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Saxty G, Squires MS, Murray CW, Berdini V, Ward GA, Miller D, Rich SJ, Cleasby A, Saalau-Bethell SM, Coyle J, Madin A, Carr MG, O'Brien MA, Jones CG, Vickerstaff E, Nijjar RK, Graham B, Pike A, Lewis EJ, Perera T, Angibaud P, Newell H. Abstract 5778: Fragment-based drug discovery of selective inhibitors of fibroblast growth factor receptor (FGFr). Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-5778] [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
Recent data in a number of tumour types has implicated Fibroblast Growth Factor (FGF) and Fibroblast Growth Factor receptor (FGFr) signalling as being key to the molecular pathology of cancer. This poster will describe fragment based drug discovery using biophysical screening to identify initial fragments. Subsequently, in the fragments-to-leads stage a detailed structural understanding of the binding interactions between the fragment and its target protein utilised X-ray crystallography and NMR. Starting with different fragments allows several lead series to be identified, often by synthesizing only small numbers of compounds.
A fragment screening campaign was conducted against the FGFr-1 to detect very low molecular weight compounds that bound to the hinge region of the kinase. The screening produced several fragment molecules (Molecular Weight <250 Da) which were in the micromolar range and confirmed binding mode in X-ray crystallography. One X-ray hit series that was 120 uM verse FGFr-3 will be described. Several iterations of structure-guided medicinal chemistry led to the identification of a lead compound with 3 nM affinity for FGFr-3, good cell activity and 30-fold selectivity verse VEGFr-2 with good oral activity. The lead was optimised to afford a compound that showed good PK/PD and efficacy.
This poster represents first disclosure of the structure of the lead series and illustrates how a fragment-based drug discovery approach can be efficiently used to discover compounds advanced nanomolar compounds with oral bioavailability.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5778.
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Affiliation(s)
| | | | - C W. Murray
- 1Astex Therapeutics, Cambridge, United Kingdom
| | - V Berdini
- 1Astex Therapeutics, Cambridge, United Kingdom
| | - G A. Ward
- 1Astex Therapeutics, Cambridge, United Kingdom
| | - D Miller
- 1Astex Therapeutics, Cambridge, United Kingdom
| | - S J. Rich
- 1Astex Therapeutics, Cambridge, United Kingdom
| | - A Cleasby
- 1Astex Therapeutics, Cambridge, United Kingdom
| | | | - J Coyle
- 1Astex Therapeutics, Cambridge, United Kingdom
| | - A Madin
- 1Astex Therapeutics, Cambridge, United Kingdom
| | - M G. Carr
- 1Astex Therapeutics, Cambridge, United Kingdom
| | | | | | | | - R K. Nijjar
- 1Astex Therapeutics, Cambridge, United Kingdom
| | - B Graham
- 1Astex Therapeutics, Cambridge, United Kingdom
| | - A Pike
- 1Astex Therapeutics, Cambridge, United Kingdom
| | - E J. Lewis
- 1Astex Therapeutics, Cambridge, United Kingdom
| | - T Perera
- 2Ortho Biotech Oncology R&D, Beerse, Belgium
| | - P Angibaud
- 2Ortho Biotech Oncology R&D, Beerse, Belgium
| | - H Newell
- 3Northern Institute for Cancer Research, Newcastle, United Kingdom
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24
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Howard S, Berdini V, Boulstridge JA, Carr MG, Cross DM, Curry J, Devine LA, Early TR, Fazal L, Gill AL, Heathcote M, Maman S, Matthews JE, McMenamin RL, Navarro EF, O’Brien MA, O’Reilly M, Rees DC, Reule M, Tisi D, Williams G, Vinković M, Wyatt PG. Fragment-Based Discovery of the Pyrazol-4-yl Urea (AT9283), a Multitargeted Kinase Inhibitor with Potent Aurora Kinase Activity. J Med Chem 2008; 52:379-88. [DOI: 10.1021/jm800984v] [Citation(s) in RCA: 250] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Steven Howard
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - Valerio Berdini
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - John A. Boulstridge
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - Maria G. Carr
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - David M. Cross
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - Jayne Curry
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - Lindsay A. Devine
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - Theresa R. Early
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - Lynsey Fazal
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - Adrian L. Gill
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - Michelle Heathcote
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - Sarita Maman
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - Julia E. Matthews
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - Rachel L. McMenamin
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - Eva F. Navarro
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - Michael A. O’Brien
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - Marc O’Reilly
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - David C. Rees
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - Matthias Reule
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - Dominic Tisi
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - Glyn Williams
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - Mladen Vinković
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
| | - Paul G. Wyatt
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, U.K
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25
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Wyatt PG, Woodhead AJ, Berdini V, Boulstridge JA, Carr MG, Cross DM, Davis DJ, Devine LA, Early TR, Feltell RE, Lewis EJ, McMenamin RL, Navarro EF, O'Brien MA, O'Reilly M, Reule M, Saxty G, Seavers LCA, Smith DM, Squires MS, Trewartha G, Walker MT, Woolford AJA. Identification of N-(4-piperidinyl)-4-(2,6-dichlorobenzoylamino)-1H-pyrazole-3-carboxamide (AT7519), a novel cyclin dependent kinase inhibitor using fragment-based X-ray crystallography and structure based drug design. J Med Chem 2008; 51:4986-99. [PMID: 18656911 DOI: 10.1021/jm800382h] [Citation(s) in RCA: 261] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The application of fragment-based screening techniques to cyclin dependent kinase 2 (CDK2) identified multiple (>30) efficient, synthetically tractable small molecule hits for further optimization. Structure-based design approaches led to the identification of multiple lead series, which retained the key interactions of the initial binding fragments and additionally explored other areas of the ATP binding site. The majority of this paper details the structure-guided optimization of indazole (6) using information gained from multiple ligand-CDK2 cocrystal structures. Identification of key binding features for this class of compounds resulted in a series of molecules with low nM affinity for CDK2. Optimisation of cellular activity and characterization of pharmacokinetic properties led to the identification of 33 (AT7519), which is currently being evaluated in clinical trials for the treatment of human cancers.
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Affiliation(s)
- Paul G Wyatt
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom.
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26
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Saxty G, Woodhead SJ, Berdini V, Davies TG, Verdonk ML, Wyatt PG, Boyle RG, Barford D, Downham R, Garrett MD, Carr RA. Identification of inhibitors of protein kinase B using fragment-based lead discovery. J Med Chem 2007; 50:2293-6. [PMID: 17451234 DOI: 10.1021/jm070091b] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using fragment-based screening techniques, 5-methyl-4-phenyl-1H-pyrazole (IC50 80 microM) was identified as a novel, low molecular weight inhibitor of protein kinase B (PKB). Herein we describe the rapid elaboration of highly potent and ligand efficient analogues using a fragment growing approach. Iterative structure-based design was supported by protein-ligand structure determinations using a PKA-PKB "chimera" and a final protein-ligand structure of a lead compound in PKBbeta itself.
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27
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Donald A, McHardy T, Rowlands MG, Hunter LJK, Davies TG, Berdini V, Boyle RG, Aherne GW, Garrett MD, Collins I. Rapid evolution of 6-phenylpurine inhibitors of protein kinase B through structure-based design. J Med Chem 2007; 50:2289-92. [PMID: 17451235 DOI: 10.1021/jm0700924] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
6-phenylpurines were identified as novel, ATP-competitive inhibitors of protein kinase B (PKB/Akt) from a fragment-based screen and were rapidly progressed to potent compounds using iterative protein-ligand crystallography with a PKA-PKB chimeric protein. An elaborated lead compound showed cell growth inhibition and effects on cellular signaling pathways characteristic of PKB inhibition.
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28
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Collins I, Caldwell J, Fonseca T, Donald A, Bavetsias V, Hunter LJK, Garrett MD, Rowlands MG, Aherne GW, Davies TG, Berdini V, Woodhead SJ, Davis D, Seavers LCA, Wyatt PG, Workman P, McDonald E. Structure-based design of isoquinoline-5-sulfonamide inhibitors of protein kinase B. Bioorg Med Chem 2005; 14:1255-73. [PMID: 16249095 DOI: 10.1016/j.bmc.2005.09.055] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [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: 06/10/2005] [Revised: 09/08/2005] [Accepted: 09/23/2005] [Indexed: 11/28/2022]
Abstract
Structure-based drug design of novel isoquinoline-5-sulfonamide inhibitors of PKB as potential antitumour agents was investigated. Constrained pyrrolidine analogues that mimicked the bound conformation of linear prototypes were identified and investigated by co-crystal structure determinations with the related protein PKA. Detailed variation in the binding modes between inhibitors with similar overall conformations was observed. Potent PKB inhibitors from this series inhibited GSK3beta phosphorylation in cellular assays, consistent with inhibition of PKB kinase activity in cells.
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Affiliation(s)
- Ian Collins
- Cancer Research, UK Centre for Cancer Therapeutics, The Institute of Cancer Research, Sutton, Surrey.
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Allegretti M, Bertini R, Cesta MC, Bizzarri C, Di Bitondo R, Di Cioccio V, Galliera E, Berdini V, Topai A, Zampella G, Russo V, Di Bello N, Nano G, Nicolini L, Locati M, Fantucci P, Florio S, Colotta F. 2-Arylpropionic CXC Chemokine Receptor 1 (CXCR1) Ligands as Novel Noncompetitive CXCL8 Inhibitors. J Med Chem 2005; 48:4312-31. [PMID: 15974585 DOI: 10.1021/jm049082i] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The CXC chemokine CXCL8/IL-8 plays a major role in the activation and recruitment of polymorphonuclear (PMN) cells at inflammatory sites. CXCL8 activates PMNs by binding the seven-transmembrane (7-TM) G-protein-coupled receptors CXC chemokine receptor 1 (CXCR1) and CXC chemokine receptor 2 (CXCR2). (R)-Ketoprofen (1) was previously reported to be a potent and specific noncompetitive inhibitor of CXCL8-induced human PMNs chemotaxis. We report here molecular modeling studies showing a putative interaction site of 1 in the TM region of CXCR1. The binding model was confirmed by alanine scanning mutagenesis and photoaffinity labeling experiments. The molecular model driven medicinal chemistry optimization of 1 led to a new class of potent and specific inhibitors of CXCL8 biological activity. Among these, repertaxin (13) was selected as a clinical candidate drug for prevention of post-ischemia reperfusion injury.
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Affiliation(s)
- Marcello Allegretti
- Dompé Research and Development, Dompé S.p.A., via Campo di Pile, 67100, L'Aquila, Italy.
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Wyatt P, Barford D, Davies T, Woodhead S, Saxty G, Davis D, Garrett M, Raynaud F, Eccles S, Berdini V. 332 Fragment-based and structure based optimisation of potent PKB/AKT inhibitors. EJC Suppl 2004. [DOI: 10.1016/s1359-6349(04)80339-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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31
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Verdonk ML, Berdini V, Hartshorn MJ, Mooij WTM, Murray CW, Taylor RD, Watson P. Virtual Screening Using Protein−Ligand Docking: Avoiding Artificial Enrichment. ACTA ACUST UNITED AC 2004; 44:793-806. [PMID: 15154744 DOI: 10.1021/ci034289q] [Citation(s) in RCA: 320] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This study addresses a number of topical issues around the use of protein-ligand docking in virtual screening. We show that, for the validation of such methods, it is key to use focused libraries (containing compounds with one-dimensional properties, similar to the actives), rather than "random" or "drug-like" libraries to test the actives against. We also show that, to obtain good enrichments, the docking program needs to produce reliable binding modes. We demonstrate how pharmacophores can be used to guide the dockings and improve enrichments, and we compare the performance of three consensus-ranking protocols against ranking based on individual scoring functions. Finally, we show that protein-ligand docking can be an effective aid in the screening for weak, fragment-like binders, which has rapidly become a popular strategy for hit identification. All results presented are based on carefully constructed virtual screening experiments against four targets, using the protein-ligand docking program GOLD.
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Affiliation(s)
- Marcel L Verdonk
- Astex Technology Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom.
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Brandolini L, Allegretti M, Berdini V, Cervellera MN, Mascagni P, Rinaldi M, Melillo G, Ghezzi P, Mengozzi M, Bertini R. Carbocysteine lysine salt monohydrate (SCMC-LYS) is a selective scavenger of reactive oxygen intermediates (ROIs). Eur Cytokine Netw 2003; 14:20-6. [PMID: 12799210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Carbocysteine lysine salt monohydrate (SCMC-Lys) is a well-known mucoactive drug whose therapeutic efficacy is commonly related to the ability of SCMC-Lys to replace fucomucins by sialomucins. The aim of this study was to determine if SCMC-Lys could exert an anti-oxidant action by scavenging reactive oxygen intermediates (ROIs). Our results show that SCMC-Lys proved effective as a selective scavenger of hypochlorous acid (HOCl) and hydroxyl radical (OH.), this effect being related to the reactivity of the SCMC tioether group. The scavenger activity of SCMC-Lys was observed in free cellular system as well as in activated human polymorphonuclear neutrophils (PMNs). SCMC-Lys scavenger activity on HOCl was paralleled by a powerful protection from HOCl-mediated inactivation of alpha1-antitripsin (alpha1-AT) inhibitor, the main serum protease inhibitor. Production of interleukin-(IL-)8, a major mediator of PMN recruitment in inflammatory diseases, is known to be mediated by intracellular OH. SCMC-Lys significantly reduced IL-8 production on stimulated human peripheral blood mononuclear cells (PBMCs) in the same range of concentrations affecting OH. activity. It is concluded that SCMC-Lys could exert, in addition to its mucoactive capacity, an anti-oxidant action, thus contributing to the therapeutic efficacy of SCMC-Lys.
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Affiliation(s)
- Laura Brandolini
- Dompé SpA Research Center, via Campo di Pile, 67100 - L'Aquila, Italy
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Quyoum R, Berdini V, Turner ML, Long HC, Maitlis PM. Mechanistic Studies of Methylene Chain Propagation in the Fischer–Tropsch Synthesis. J Catal 1998. [DOI: 10.1006/jcat.1997.1927] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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35
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Quyoum R, Berdini V, Turner ML, Long HC, Maitlis PM. Carbon Monoxide Hydrogenation: Intermediates Derived from Methylene Probes Offering Dual Polymerization Pathways in Fischer−Tropsch Homologation. J Am Chem Soc 1996. [DOI: 10.1021/ja961899g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ruhksana Quyoum
- Department of Chemistry The University of Sheffield Sheffield S3 7HF, U.K
| | - Valerio Berdini
- Department of Chemistry The University of Sheffield Sheffield S3 7HF, U.K
| | - Michael L. Turner
- Department of Chemistry The University of Sheffield Sheffield S3 7HF, U.K
| | - Helen C. Long
- Department of Chemistry The University of Sheffield Sheffield S3 7HF, U.K
| | - Peter M. Maitlis
- Department of Chemistry The University of Sheffield Sheffield S3 7HF, U.K
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Macarri G, Feliciangeli G, Berdini V, Jezequel AM, Benedetti A. Canalicular cholestasis due to amiodarone toxicity. A definite diagnosis obtained by electron microscopy. Ital J Gastroenterol 1995; 27:436-8. [PMID: 8775470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A case of jaundice due to canalicular cholestasis during amiodarone therapy is reported. A definite diagnosis was attained by ultrastructural evidence of a phospholipidosis pattern, a characteristic amiodarone-induced injury. Jaundice occurred within the third month of therapy. Serum bilirubin levels continued to increase in the two weeks following drug withdrawal. A slow decrease was observed in the following three months. Only four cases of jaundice associated with amiodarone therapy have been reported until now.
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Affiliation(s)
- G Macarri
- Clinica di Gastroenterologia e Cattedra di Citopatologia, Università di Ancona, Italy
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