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Kuki N, Walmsley DL, Kanai K, Takechi S, Yoshida M, Murakami R, Takano K, Tominaga Y, Takahashi M, Ito S, Nakao N, Angove H, Baker LM, Carter E, Dokurno P, Le Strat L, Macias AT, Molyneaux CA, Murray JB, Surgenor AE, Hamada T, Hubbard RE. A covalent fragment-based strategy targeting a novel cysteine to inhibit activity of mutant EGFR kinase. RSC Med Chem 2023; 14:2731-2737. [PMID: 38107172 PMCID: PMC10718517 DOI: 10.1039/d3md00439b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/17/2023] [Indexed: 12/19/2023] Open
Abstract
Several generations of ATP-competitive anti-cancer drugs that inhibit the activity of the intracellular kinase domain of the epidermal growth factor receptor (EGFR) have been developed over the past twenty years. The first-generation of drugs such as gefitinib bind reversibly and were followed by a second-generation such as dacomitinib that harbor an acrylamide moiety that forms a covalent bond with C797 in the ATP binding pocket. Resistance emerges through mutation of the T790 gatekeeper residue to methionine, which introduces steric hindrance to drug binding and increases the Km for ATP. A third generation of drugs, such as osimertinib were developed which were effective against T790M EGFR in which an acrylamide moiety forms a covalent bond with C797, although resistance has emerged by mutation to S797. A fragment-based screen to identify new starting points for an EGFR inhibitor serendipitously identified a fragment that reacted with C775, a previously unexploited residue in the ATP binding pocket for a covalent inhibitor to target. A number of acrylamide containing fragments were identified that selectively reacted with C775. One of these acrylamides was optimized to a highly selective inhibitor with sub-1 μM activity, that is active against T790M, C797S mutant EGFR independent of ATP concentration, providing a potential new strategy for pan-EGFR mutant inhibition.
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Affiliation(s)
- Naoki Kuki
- R&D Division Daiichi Sankyo Co., Ltd. Shinagawa-ku Tokyo 140-8710 Japan
| | | | - Kazuo Kanai
- R&D Division Daiichi Sankyo Co., Ltd. Shinagawa-ku Tokyo 140-8710 Japan
| | - Sho Takechi
- R&D Division Daiichi Sankyo Co., Ltd. Shinagawa-ku Tokyo 140-8710 Japan
| | - Masao Yoshida
- R&D Division Daiichi Sankyo Co., Ltd. Shinagawa-ku Tokyo 140-8710 Japan
| | - Ryo Murakami
- R&D Division Daiichi Sankyo Co., Ltd. Shinagawa-ku Tokyo 140-8710 Japan
| | - Kohei Takano
- R&D Division Daiichi Sankyo Co., Ltd. Shinagawa-ku Tokyo 140-8710 Japan
| | - Yuichi Tominaga
- R&D Division Daiichi Sankyo Co., Ltd. Shinagawa-ku Tokyo 140-8710 Japan
| | - Mizuki Takahashi
- Daiichi Sankyo RD Novare Co., Ltd. Edogawa-ku Tokyo 134-8630 Japan
| | - Shuichiro Ito
- Daiichi Sankyo RD Novare Co., Ltd. Edogawa-ku Tokyo 134-8630 Japan
| | - Naoki Nakao
- Daiichi Sankyo RD Novare Co., Ltd. Edogawa-ku Tokyo 134-8630 Japan
| | - Hayley Angove
- Vernalis (R&D) Ltd., Granta Park Cambridge CB21 6GB UK
| | - Lisa M Baker
- Vernalis (R&D) Ltd., Granta Park Cambridge CB21 6GB UK
| | - Edward Carter
- Vernalis (R&D) Ltd., Granta Park Cambridge CB21 6GB UK
| | - Pawel Dokurno
- Vernalis (R&D) Ltd., Granta Park Cambridge CB21 6GB UK
| | - Loic Le Strat
- Vernalis (R&D) Ltd., Granta Park Cambridge CB21 6GB UK
| | - Alba T Macias
- Vernalis (R&D) Ltd., Granta Park Cambridge CB21 6GB UK
| | | | | | | | - Tomoaki Hamada
- R&D Division Daiichi Sankyo Co., Ltd. Shinagawa-ku Tokyo 140-8710 Japan
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Brough PA, Baker L, Bedford S, Brown K, Chavda S, Chell V, D'Alessandro J, Davies NGM, Davis B, Le Strat L, Macias AT, Maddox D, Mahon PC, Massey AJ, Matassova N, McKenna S, Meissner JWG, Moore JD, Murray JB, Northfield CJ, Parry C, Parsons R, Roughley SD, Shaw T, Simmonite H, Stokes S, Surgenor A, Stefaniak E, Robertson A, Wang Y, Webb P, Whitehead N, Wood M. Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase. J Med Chem 2017; 60:2271-2286. [PMID: 28199108 DOI: 10.1021/acs.jmedchem.6b01478] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Libraries of nonpurified resorcinol amide derivatives were screened by surface plasmon resonance (SPR) to determine the binding dissociation constant (off-rate, kd) for compounds binding to the pyruvate dehydrogenase kinase (PDHK) enzyme. Parallel off-rate measurements against HSP90 and application of structure-based drug design enabled rapid hit to lead progression in a program to identify pan-isoform ATP-competitive inhibitors of PDHK. Lead optimization identified selective sub-100-nM inhibitors of the enzyme which significantly reduced phosphorylation of the E1α subunit in the PC3 cancer cell line in vitro.
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Affiliation(s)
- Paul A Brough
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Lisa Baker
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Simon Bedford
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Kirsten Brown
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Seema Chavda
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Victoria Chell
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | | | | | - Ben Davis
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Loic Le Strat
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Alba T Macias
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Daniel Maddox
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Patrick C Mahon
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Andrew J Massey
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Natalia Matassova
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Sean McKenna
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | | | - Jonathan D Moore
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - James B Murray
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | | | - Charles Parry
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Rachel Parsons
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Stephen D Roughley
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Terry Shaw
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Heather Simmonite
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Stephen Stokes
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Allan Surgenor
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Emma Stefaniak
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Alan Robertson
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Yikang Wang
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Paul Webb
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Neil Whitehead
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Mike Wood
- Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K
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James PL, Le Strat L, Ellervik U, Bratwall C, Nordén B, Brown T, Fox KR. Effects of a hairpin polyamide on DNA melting: comparison with distamycin and Hoechst 33258. Biophys Chem 2004; 111:205-12. [PMID: 15501563 DOI: 10.1016/j.bpc.2004.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [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: 02/02/2004] [Revised: 06/01/2004] [Accepted: 06/01/2004] [Indexed: 11/15/2022]
Abstract
We have used DNase I footprinting and fluorescence melting studies to study the interaction of the hairpin polyamide Im-Py-Py-Py-(R)H2Ngamma-Im-Py-Py-Py-beta-Dp with its preferred binding sites (5'-WGWWCW; W=A or T) and other sequences. DNase I footprinting confirmed that the ligand binds to the sequence AGAACA at nanomolar concentrations and that changing the terminal A to G causes a dramatic decrease in affinity, while there was no interaction with the reverse sequence WCWWGW. Fluorescence melting studies with 11-mer duplexes showed that the polyamide had very different effects on the forward (TGWWCT) and reverse (TCTAGT) sequences. At low concentrations, the polyamide produced biphasic melting curves with TGATCT, TGTACT and TGAACT, suggesting a strong interaction. In contrast, the melting profiles with TCTAGT were always monophasic and showed much smaller concentration dependent changes in Tm. The polyamide also showed weak binding to the sequence TGATCT when one of the central AT pairs was replaced with an AC mismatch. These melting profiles were compared with those produced by the AT-selective minor groove binding agents distamycin and Hoechst 33258 at the same sites and at similar sequences containing A5 and (AT)3, which are expected to bind distamycin in the 1:1 and 2:1 modes, respectively. These ligands produced simple monophasic melting curves in which the Tm steadily increased as the ligand concentration was raised.
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Affiliation(s)
- Peter L James
- Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
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