1
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Kettle JG, Bagal SK, Barratt D, Bodnarchuk MS, Boyd S, Braybrooke E, Breed J, Cassar DJ, Cosulich S, Davies M, Davies NL, Deng C, Eatherton A, Evans L, Feron LJ, Fillery S, Gleave ES, Goldberg FW, Cortés González MA, Guerot C, Haider A, Harlfinger S, Howells R, Jackson A, Johnström P, Kemmitt PD, Koers A, Kondrashov M, Lamont GM, Lamont S, Lewis HJ, Liu L, Mylrea M, Nash S, Niedbala MJ, Peter A, Phillips C, Pike K, Raubo P, Robb GR, Ross S, Sanders MG, Schou M, Simpson I, Steward O. Discovery of AZD4747, a Potent and Selective Inhibitor of Mutant GTPase KRAS G12C with Demonstrable CNS Penetration. J Med Chem 2023. [PMID: 37395055 DOI: 10.1021/acs.jmedchem.3c00746] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The glycine to cysteine mutation at codon 12 of Kirsten rat sarcoma (KRAS) represents an Achilles heel that has now rendered this important GTPase druggable. Herein, we report our structure-based drug design approach that led to the identification of 14, AZD4747, a clinical development candidate for the treatment of KRASG12C-positive tumors, including the treatment of central nervous system (CNS) metastases. Building on our earlier discovery of C5-tethered quinazoline AZD4625, excision of a usually critical pyrimidine ring yielded a weak but brain-penetrant start point which was optimized for potency and DMPK. Key design principles and measured parameters that give high confidence in CNS exposure are discussed. During optimization, divergence between rodent and non-rodent species was observed in CNS exposure, with primate PET studies ultimately giving high confidence in the expected translation to patients. AZD4747 is a highly potent and selective inhibitor of KRASG12C with an anticipated low clearance and high oral bioavailability profile in humans.
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Affiliation(s)
| | | | - Derek Barratt
- Discovery Sciences, R&D, AstraZeneca,, Cambridge CB4 0WG, U.K
| | | | - Scott Boyd
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Jason Breed
- Discovery Sciences, R&D, AstraZeneca,, Cambridge CB4 0WG, U.K
| | | | | | | | | | - Chao Deng
- Pharmaron Beijing Co., Ltd. 6 Taihe Road BDA, Beijing 100176, P. R. China
| | | | - Laura Evans
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | - Emma S Gleave
- Discovery Sciences, R&D, AstraZeneca,, Cambridge CB4 0WG, U.K
| | | | - Miguel A Cortés González
- Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet and Stockholm County Council, Stockholm SE-171 76, Sweden
| | | | - Afreen Haider
- Discovery Sciences, R&D, AstraZeneca,, Cambridge CB4 0WG, U.K
| | | | | | - Anne Jackson
- Discovery Sciences, R&D, AstraZeneca,, Cambridge CB4 0WG, U.K
| | - Peter Johnström
- PET Science Centre, Precision Medicine and Biosamples, Oncology R&D, AstraZeneca, Karolinska Institutet, Stockholm SE-171 76, Sweden
- Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet and Stockholm County Council, Stockholm SE-171 76, Sweden
| | | | - Alex Koers
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Mikhail Kondrashov
- Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet and Stockholm County Council, Stockholm SE-171 76, Sweden
| | | | - Scott Lamont
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Libin Liu
- Pharmaron Beijing Co., Ltd. 6 Taihe Road BDA, Beijing 100176, P. R. China
| | - Megan Mylrea
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Samuel Nash
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Alison Peter
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Kurt Pike
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Piotr Raubo
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Sarah Ross
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Magnus Schou
- PET Science Centre, Precision Medicine and Biosamples, Oncology R&D, AstraZeneca, Karolinska Institutet, Stockholm SE-171 76, Sweden
- Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet and Stockholm County Council, Stockholm SE-171 76, Sweden
| | - Iain Simpson
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
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2
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Cumming IA, Degorce SL, Aagaard A, Braybrooke EL, Davies NL, Diène CR, Eatherton AJ, Felstead HR, Groombridge SD, Lenz EM, Li Y, Nai Y, Pearson S, Robb GR, Scott JS, Steward OR, Wu C, Xue Y, Zhang L, Zhang Y. Identification and optimisation of a pyrimidopyridone series of IRAK4 inhibitors. Bioorg Med Chem 2022; 63:116729. [PMID: 35439688 DOI: 10.1016/j.bmc.2022.116729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 01/13/2022] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 12/01/2022]
Abstract
In this article, we report the discovery of a series of pyrimidopyridones as inhibitors of IRAK4 kinase. From a previously disclosed 5-azaquinazoline series, we found that switching the pyridine ring for an N-substituted pyridone gave a novel hinge binding scaffold which retained potency against IRAK4. Importantly, introduction of the carbonyl established an internal hydrogen bond with the 4-NH, establishing a conformational lock and allowing truncation of the large basic substituent to a 1-methylcyclopyl group. Subsequent optimisation, facilitated by X-ray crystal structures, allowed identification of preferred substituents at both the pyridone core and pyrazole. Subsequent combinations of optimal groups allowed control of lipophilicity and identification of potent and selective inhibitors of IRAK4 with better in vitro permeability and lower clearance.
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Affiliation(s)
- Iain A Cumming
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, United Kingdom.
| | - Sébastien L Degorce
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, United Kingdom
| | - Anna Aagaard
- Discovery Sciences, R&D, AstraZeneca, Gothenburg, SE-431 83 Mölndal, Sweden
| | - Erin L Braybrooke
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, United Kingdom
| | - Nichola L Davies
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, United Kingdom
| | - Coura R Diène
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, United Kingdom
| | - Andrew J Eatherton
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, United Kingdom
| | - Hannah R Felstead
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, United Kingdom
| | - Sam D Groombridge
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, United Kingdom
| | - Eva M Lenz
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, United Kingdom
| | - Yunxia Li
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176 PR China
| | - Youfeng Nai
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176 PR China
| | - Stuart Pearson
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, United Kingdom
| | - Graeme R Robb
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, United Kingdom
| | - James S Scott
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, United Kingdom
| | - Oliver R Steward
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, United Kingdom
| | - Chengyan Wu
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176 PR China
| | - Yafeng Xue
- Discovery Sciences, R&D, AstraZeneca, Gothenburg, SE-431 83 Mölndal, Sweden
| | - Lanping Zhang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176 PR China
| | - Yanxiu Zhang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176 PR China
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3
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Kettle JG, Bagal SK, Bickerton S, Bodnarchuk MS, Boyd S, Breed J, Carbajo RJ, Cassar DJ, Chakraborty A, Cosulich S, Cumming I, Davies M, Davies NL, Eatherton A, Evans L, Feron L, Fillery S, Gleave ES, Goldberg FW, Hanson L, Harlfinger S, Howard M, Howells R, Jackson A, Kemmitt P, Lamont G, Lamont S, Lewis HJ, Liu L, Niedbala MJ, Phillips C, Polanski R, Raubo P, Robb G, Robinson DM, Ross S, Sanders MG, Tonge M, Whiteley R, Wilkinson S, Yang J, Zhang W. Discovery of AZD4625, a Covalent Allosteric Inhibitor of the Mutant GTPase KRAS G12C. J Med Chem 2022; 65:6940-6952. [PMID: 35471939 DOI: 10.1021/acs.jmedchem.2c00369] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
KRAS is an archetypal high-value intractable oncology drug target. The glycine to cysteine mutation at codon 12 represents an Achilles heel that has now rendered this important GTPase druggable. Herein, we report our structure-based drug design approach that led to the identification of 21, AZD4625, a clinical development candidate for the treatment of KRASG12C positive tumors. Highlights include a quinazoline tethering strategy to lock out a bio-relevant binding conformation and an optimization strategy focused on the reduction of extrahepatic clearance mechanisms seen in preclinical species. Crystallographic analysis was also key in helping to rationalize unusual structure-activity relationship in terms of ring size and enantio-preference. AZD4625 is a highly potent and selective inhibitor of KRASG12C with an anticipated low clearance and high oral bioavailability profile in humans.
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Affiliation(s)
| | | | | | | | - Scott Boyd
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Jason Breed
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | | | | | - Iain Cumming
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | | | - Laura Evans
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Lyman Feron
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Emma S Gleave
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | | | | | | | - Anne Jackson
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Paul Kemmitt
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Scott Lamont
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Libin Liu
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
| | | | | | - Radek Polanski
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Piotr Raubo
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Graeme Robb
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Sarah Ross
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Michael Tonge
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | - Junsheng Yang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
| | - Wenman Zhang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
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4
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Winter-Holt JJ, Bardelle C, Chiarparin E, Dale IL, Davey PRJ, Davies NL, Denz C, Fillery SM, Guérot CM, Han F, Hughes SJ, Kulkarni M, Liu Z, Milbradt A, Moss TA, Niu H, Patel J, Rabow AA, Schimpl M, Shi J, Sun D, Yang D, Guichard S. Discovery of a Potent and Selective ATAD2 Bromodomain Inhibitor with Antiproliferative Activity in Breast Cancer Models. J Med Chem 2022; 65:3306-3331. [PMID: 35133824 DOI: 10.1021/acs.jmedchem.1c01871] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
ATAD2 is an epigenetic bromodomain-containing target which is overexpressed in many cancers and has been suggested as a potential oncology target. While several small molecule inhibitors have been described in the literature, their cellular activity has proved to be underwhelming. In this work, we describe the identification of a novel series of ATAD2 inhibitors by high throughput screening, confirmation of the bromodomain region as the site of action, and the optimization campaign undertaken to improve the potency, selectivity, and permeability of the initial hit. The result is compound 5 (AZ13824374), a highly potent and selective ATAD2 inhibitor which shows cellular target engagement and antiproliferative activity in a range of breast cancer models.
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Affiliation(s)
| | - Catherine Bardelle
- BioPharmaceuticals R&D, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom
| | | | | | | | | | - Christopher Denz
- Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | | | | | - Fujin Han
- Pharmaron Beijing Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | | | - Meghana Kulkarni
- Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Zhaoqun Liu
- Pharmaron Beijing Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | | | | | - Huijun Niu
- Pharmaron Beijing Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | | | | | | | - Junjie Shi
- Pharmaron Beijing Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Dongqing Sun
- Pharmaron Beijing Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Dejian Yang
- Pharmaron Beijing Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Sylvie Guichard
- Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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5
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McCoull W, Boyd S, Brown MR, Coen M, Collingwood O, Davies NL, Doherty A, Fairley G, Goldberg K, Hardaker E, He G, Hennessy EJ, Hopcroft P, Hodgson G, Jackson A, Jiang X, Karmokar A, Lainé AL, Lindsay N, Mao Y, Markandu R, McMurray L, McLean N, Mooney L, Musgrove H, Nissink JWM, Pflug A, Reddy VP, Rawlins PB, Rivers E, Schimpl M, Smith GF, Tentarelli S, Travers J, Troup RI, Walton J, Wang C, Wilkinson S, Williamson B, Winter-Holt J, Yang D, Zheng Y, Zhu Q, Smith PD. Optimization of an Imidazo[1,2- a]pyridine Series to Afford Highly Selective Type I1/2 Dual Mer/Axl Kinase Inhibitors with In Vivo Efficacy. J Med Chem 2021; 64:13524-13539. [PMID: 34478292 DOI: 10.1021/acs.jmedchem.1c00920] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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
Inhibition of Mer and Axl kinases has been implicated as a potential way to improve the efficacy of current immuno-oncology therapeutics by restoring the innate immune response in the tumor microenvironment. Highly selective dual Mer/Axl kinase inhibitors are required to validate this hypothesis. Starting from hits from a DNA-encoded library screen, we optimized an imidazo[1,2-a]pyridine series using structure-based compound design to improve potency and reduce lipophilicity, resulting in a highly selective in vivo probe compound 32. We demonstrated dose-dependent in vivo efficacy and target engagement in Mer- and Axl-dependent efficacy models using two structurally differentiated and selective dual Mer/Axl inhibitors. Additionally, in vivo efficacy was observed in a preclinical MC38 immuno-oncology model in combination with anti-PD1 antibodies and ionizing radiation.
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Affiliation(s)
| | - Scott Boyd
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Martin R Brown
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Muireann Coen
- Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | - Ann Doherty
- Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Gary Fairley
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | - Guang He
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
| | - Edward J Hennessy
- Oncology R&D, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Philip Hopcroft
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - George Hodgson
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Anne Jackson
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Xiefeng Jiang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
| | - Ankur Karmokar
- Oncology R&D, AstraZeneca, Mereside, Alderley Park, Macclesfield SK10 4TG, U.K
| | - Anne-Laure Lainé
- Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Yumeng Mao
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | | | - Lorraine Mooney
- Oncology R&D, AstraZeneca, Mereside, Alderley Park, Macclesfield SK10 4TG, U.K
| | - Helen Musgrove
- Oncology R&D, AstraZeneca, Mereside, Alderley Park, Macclesfield SK10 4TG, U.K
| | | | - Alexander Pflug
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Venkatesh Pilla Reddy
- Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Emma Rivers
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Graham F Smith
- Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Sharon Tentarelli
- Oncology R&D, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Jon Travers
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | - Cheng Wang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
| | | | | | | | - Dejian Yang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
| | - Yuting Zheng
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
| | - Qianxiu Zhu
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
| | - Paul D Smith
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
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6
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Balazs AYS, Carbajo RJ, Davies NL, Dong Y, Hird AW, Johannes JW, Lamb ML, McCoull W, Raubo P, Robb GR, Packer MJ, Chiarparin E. Correction to "Free Ligand 1D NMR Conformational Signatures To Enhance Structure Based Drug Design of a Mcl-1 Inhibitor (AZD5991) and Other Synthetic Macrocycles". J Med Chem 2021; 64:2849. [PMID: 33646774 DOI: 10.1021/acs.jmedchem.1c00273] [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: 11/29/2022]
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7
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Balazs AYS, Carbajo RJ, Davies NL, Dong Y, Hird AW, Johannes JW, Lamb ML, McCoull W, Raubo P, Robb GR, Packer MJ, Chiarparin E. Free Ligand 1D NMR Conformational Signatures To Enhance Structure Based Drug Design of a Mcl-1 Inhibitor (AZD5991) and Other Synthetic Macrocycles. J Med Chem 2019; 62:9418-9437. [PMID: 31361481 DOI: 10.1021/acs.jmedchem.9b00716] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The three-dimensional conformations adopted by a free ligand in solution impact bioactivity and physicochemical properties. Solution 1D NMR spectra inherently contain information on ligand conformational flexibility and three-dimensional shape, as well as the propensity of the free ligand to fully preorganize into the bioactive conformation. Herein we discuss some key learnings, distilled from our experience developing potent and selective synthetic macrocyclic inhibitors, including Mcl-1 clinical candidate AZD5991. Case studies have been selected from recent oncology research projects, demonstrating how 1D NMR conformational signatures can complement X-ray protein-ligand structural information to guide medicinal chemistry optimization. Learning to extract free ligand conformational information from routinely available 1D NMR signatures has proven to be fast enough to guide medicinal chemistry decisions within design cycles for compound optimization.
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Affiliation(s)
- Amber Y S Balazs
- Chemistry, R&D Oncology , AstraZeneca , Waltham , Massachusetts 02451 , United States
| | - Rodrigo J Carbajo
- Chemistry, R&D Oncology , AstraZeneca , Cambridge CB4 0QA , United Kingdom
| | - Nichola L Davies
- Chemistry, R&D Oncology , AstraZeneca , Cambridge CB4 0QA , United Kingdom
| | - Yu Dong
- Pharmaron Beijing Co., Ltd. , Beijing 100176 , China
| | - Alexander W Hird
- Chemistry, R&D Oncology , AstraZeneca , Waltham , Massachusetts 02451 , United States
| | - Jeffrey W Johannes
- Chemistry, R&D Oncology , AstraZeneca , Waltham , Massachusetts 02451 , United States
| | - Michelle L Lamb
- Chemistry, R&D Oncology , AstraZeneca , Waltham , Massachusetts 02451 , United States
| | - William McCoull
- Chemistry, R&D Oncology , AstraZeneca , Cambridge CB4 0QA , United Kingdom
| | - Piotr Raubo
- Chemistry, R&D Oncology , AstraZeneca , Cambridge CB4 0QA , United Kingdom
| | - Graeme R Robb
- Chemistry, R&D Oncology , AstraZeneca , Cambridge CB4 0QA , United Kingdom
| | - Martin J Packer
- Chemistry, R&D Oncology , AstraZeneca , Cambridge CB4 0QA , United Kingdom
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8
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Pike KG, Barlaam B, Cadogan E, Campbell A, Chen Y, Colclough N, Davies NL, de-Almeida C, Degorce SL, Didelot M, Dishington A, Ducray R, Durant ST, Hassall LA, Holmes J, Hughes GD, MacFaul PA, Mulholland KR, McGuire TM, Ouvry G, Pass M, Robb G, Stratton N, Wang Z, Wilson J, Zhai B, Zhao K, Al-Huniti N. The Identification of Potent, Selective, and Orally Available Inhibitors of Ataxia Telangiectasia Mutated (ATM) Kinase: The Discovery of AZD0156 (8-{6-[3-(Dimethylamino)propoxy]pyridin-3-yl}-3-methyl-1-(tetrahydro-2H-pyran-4-yl)-1,3-dihydro-2H-imidazo[4,5-c]quinolin-2-one). J Med Chem 2018; 61:3823-3841. [DOI: 10.1021/acs.jmedchem.7b01896] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Kurt G. Pike
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Bernard Barlaam
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Elaine Cadogan
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Andrew Campbell
- Pharmaceutical Sciences, AstraZeneca, Silk Road Business Park, Macclesfield SK10 2NA, U.K
| | - Yingxue Chen
- Oncology, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Nicola Colclough
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Nichola L. Davies
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Camila de-Almeida
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Sebastien L. Degorce
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
- Oncology, IMED Biotech Unit, AstraZeneca, Centre de Recherches, Z. I. la Pompelle, BP 1050, 51689 Reims Cedex 2, France
| | - Myriam Didelot
- Oncology, IMED Biotech Unit, AstraZeneca, Centre de Recherches, Z. I. la Pompelle, BP 1050, 51689 Reims Cedex 2, France
| | - Allan Dishington
- Oncology, IMED Biotech Unit, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K
| | - Richard Ducray
- Oncology, IMED Biotech Unit, AstraZeneca, Centre de Recherches, Z. I. la Pompelle, BP 1050, 51689 Reims Cedex 2, France
| | - Stephen T. Durant
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Lorraine A. Hassall
- Oncology, IMED Biotech Unit, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K
| | - Jane Holmes
- Oncology, IMED Biotech Unit, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K
| | - Gareth D. Hughes
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Philip A. MacFaul
- Oncology, IMED Biotech Unit, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K
| | - Keith R. Mulholland
- Chemical Development, AstraZeneca, Silk Road Business Park, Macclesfield SK10 2NA, U.K
| | - Thomas M. McGuire
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Gilles Ouvry
- Oncology, IMED Biotech Unit, AstraZeneca, Centre de Recherches, Z. I. la Pompelle, BP 1050, 51689 Reims Cedex 2, France
| | - Martin Pass
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Graeme Robb
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Natalie Stratton
- Discovery Sciences, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K
| | - Zhenhua Wang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Joanne Wilson
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Baochang Zhai
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Kang Zhao
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Nidal Al-Huniti
- Oncology, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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9
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Scott JS, Degorce SL, Anjum R, Culshaw J, Davies RDM, Davies NL, Dillman KS, Dowling JE, Drew L, Ferguson AD, Groombridge SD, Halsall CT, Hudson JA, Lamont S, Lindsay NA, Marden SK, Mayo MF, Pease JE, Perkins DR, Pink JH, Robb GR, Rosen A, Shen M, McWhirter C, Wu D. Discovery and Optimization of Pyrrolopyrimidine Inhibitors of Interleukin-1 Receptor Associated Kinase 4 (IRAK4) for the Treatment of Mutant MYD88L265P Diffuse Large B-Cell Lymphoma. J Med Chem 2017; 60:10071-10091. [DOI: 10.1021/acs.jmedchem.7b01290] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- James S. Scott
- Oncology,
IMED Biotech Unit, AstraZeneca, Cambridge CB4 0FZ, United Kingdom
| | | | - Rana Anjum
- Oncology,
IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Janet Culshaw
- Oncology,
IMED Biotech Unit, AstraZeneca, Macclesfield SK10 4TG, United Kingdom
| | - Robert D. M. Davies
- Oncology,
IMED Biotech Unit, AstraZeneca, Macclesfield SK10 4TG, United Kingdom
| | - Nichola L. Davies
- Oncology,
IMED Biotech Unit, AstraZeneca, Cambridge CB4 0FZ, United Kingdom
| | - Keith S. Dillman
- Oncology,
IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - James E. Dowling
- Oncology,
IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Lisa Drew
- Oncology,
IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Andrew D. Ferguson
- Oncology,
IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Sam D. Groombridge
- Oncology,
IMED Biotech Unit, AstraZeneca, Macclesfield SK10 4TG, United Kingdom
| | | | - Julian A. Hudson
- Oncology,
IMED Biotech Unit, AstraZeneca, Macclesfield SK10 4TG, United Kingdom
| | - Scott Lamont
- Oncology,
IMED Biotech Unit, AstraZeneca, Cambridge CB4 0FZ, United Kingdom
| | - Nicola A. Lindsay
- Oncology,
IMED Biotech Unit, AstraZeneca, Cambridge CB4 0FZ, United Kingdom
| | - Stacey K. Marden
- Pharmaceutical
Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Michele F. Mayo
- Oncology,
IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - J. Elizabeth Pease
- Oncology,
IMED Biotech Unit, AstraZeneca, Cambridge CB4 0FZ, United Kingdom
| | - David R. Perkins
- Oncology,
IMED Biotech Unit, AstraZeneca, Macclesfield SK10 4TG, United Kingdom
| | - Jennifer H. Pink
- Oncology,
IMED Biotech Unit, AstraZeneca, Macclesfield SK10 4TG, United Kingdom
| | - Graeme R. Robb
- Oncology,
IMED Biotech Unit, AstraZeneca, Cambridge CB4 0FZ, United Kingdom
| | - Alan Rosen
- Oncology,
IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Minhui Shen
- Oncology,
IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Claire McWhirter
- Oncology,
IMED Biotech Unit, AstraZeneca, Cambridge CB4 0FZ, United Kingdom
| | - Dedong Wu
- Pharmaceutical
Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
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10
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Lonsdale R, Burgess J, Colclough N, Davies NL, Lenz EM, Orton AL, Ward RA. Expanding the Armory: Predicting and Tuning Covalent Warhead Reactivity. J Chem Inf Model 2017; 57:3124-3137. [PMID: 29131621 DOI: 10.1021/acs.jcim.7b00553] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Targeted covalent inhibition is an established approach for increasing the potency and selectivity of potential drug candidates, as well as identifying potent and selective tool compounds for target validation studies. It is evident that identification of reversible recognition elements is essential for selective covalent inhibition, but this must also be achieved with the appropriate level of inherent reactivity of the reactive functionality (or "warhead"). Structural changes that increase or decrease warhead reactivity, guided by methods to predict the effect of those changes, have the potential to tune warhead reactivity and negate issues related to potency and/or toxicity. The half-life to adduct formation with glutathione (GSH t1/2) is a useful assay for measuring the reactivity of cysteine-targeting covalent warheads but is limited to synthesized molecules. In this manuscript we assess the ability of several experimental and computational approaches to predict GSH t1/2 for a range of cysteine targeting warheads, including a novel method based on pKa. Furthermore, matched molecular pairs analysis has been performed against our internal compound collection, revealing structure-activity relationships between a selection of different covalent warheads. These observations and methods of prediction will be valuable in the design of new covalent inhibitors with desired levels of reactivity.
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Affiliation(s)
- Richard Lonsdale
- Chemistry and DMPK, Oncology, IMED Biotech Unit, AstraZeneca , Cambridge CB4 0WG, UK
| | - Jonathan Burgess
- Chemistry and DMPK, Oncology, IMED Biotech Unit, AstraZeneca , Cambridge CB4 0WG, UK
| | - Nicola Colclough
- Chemistry and DMPK, Oncology, IMED Biotech Unit, AstraZeneca , Cambridge CB4 0WG, UK
| | - Nichola L Davies
- Chemistry and DMPK, Oncology, IMED Biotech Unit, AstraZeneca , Cambridge CB4 0WG, UK
| | - Eva M Lenz
- Chemistry and DMPK, Oncology, IMED Biotech Unit, AstraZeneca , Cambridge CB4 0WG, UK
| | - Alexandra L Orton
- Chemistry and DMPK, Oncology, IMED Biotech Unit, AstraZeneca , Cambridge CB4 0WG, UK
| | - Richard A Ward
- Chemistry and DMPK, Oncology, IMED Biotech Unit, AstraZeneca , Cambridge CB4 0WG, UK
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11
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Fryszkowska A, Peterson J, Davies NL, Dewar C, Evans G, Bycroft M, Triggs N, Fleming T, Gorantla SSC, Hoge G, Quirmbach M, Timmanna U, Reddy Poreddy S, Kumar Reddy DN, Dahanukar V, Holt-Tiffin KE. Development of a Chemoenzymatic Process for Dehydroepiandrosterone Acetate Synthesis. Org Process Res Dev 2016. [DOI: 10.1021/acs.oprd.6b00215] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anna Fryszkowska
- Chirotech
Technology Centre, Dr. Reddy’s Laboratories EU Ltd., 410 Cambridge
Science Park, Cambridge CB4 0PE, United Kingdom
| | - Justine Peterson
- Chirotech
Technology Centre, Dr. Reddy’s Laboratories EU Ltd., 410 Cambridge
Science Park, Cambridge CB4 0PE, United Kingdom
| | - Nichola L. Davies
- Chirotech
Technology Centre, Dr. Reddy’s Laboratories EU Ltd., 410 Cambridge
Science Park, Cambridge CB4 0PE, United Kingdom
| | - Colin Dewar
- Chirotech
Technology Centre, Dr. Reddy’s Laboratories EU Ltd., 410 Cambridge
Science Park, Cambridge CB4 0PE, United Kingdom
| | - George Evans
- Chirotech
Technology Centre, Dr. Reddy’s Laboratories EU Ltd., 410 Cambridge
Science Park, Cambridge CB4 0PE, United Kingdom
| | - Matthew Bycroft
- Chirotech
Technology Centre, Dr. Reddy’s Laboratories EU Ltd., 410 Cambridge
Science Park, Cambridge CB4 0PE, United Kingdom
| | - Neil Triggs
- Chirotech
Technology Centre, Dr. Reddy’s Laboratories EU Ltd., 410 Cambridge
Science Park, Cambridge CB4 0PE, United Kingdom
| | - Toni Fleming
- Chirotech
Technology Centre, Dr. Reddy’s Laboratories EU Ltd., 410 Cambridge
Science Park, Cambridge CB4 0PE, United Kingdom
| | | | - Garrett Hoge
- Chirotech
Technology Centre, Dr. Reddy’s Laboratories EU Ltd., 410 Cambridge
Science Park, Cambridge CB4 0PE, United Kingdom
| | - Michael Quirmbach
- Dr. Reddy’s Laboratories SA Elisabethenanlage, 11CH-4051 Basel, Switzerland
| | - Upadhya Timmanna
- Custom
Pharmaceutical Services, Dr. Reddy’s Laboratories Ltd, Bollaram
Road, Miyapur, Hyderabad 500049, India
| | - Srinivas Reddy Poreddy
- Custom
Pharmaceutical Services, Dr. Reddy’s Laboratories Ltd, Bollaram
Road, Miyapur, Hyderabad 500049, India
| | - D. Naresh Kumar Reddy
- Custom
Pharmaceutical Services, Dr. Reddy’s Laboratories Ltd, Bollaram
Road, Miyapur, Hyderabad 500049, India
| | - Vilas Dahanukar
- Custom
Pharmaceutical Services, Dr. Reddy’s Laboratories Ltd, Bollaram
Road, Miyapur, Hyderabad 500049, India
| | - Karen E. Holt-Tiffin
- Chirotech
Technology Centre, Dr. Reddy’s Laboratories EU Ltd., 410 Cambridge
Science Park, Cambridge CB4 0PE, United Kingdom
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12
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Kettle JG, Alwan H, Bista M, Breed J, Davies NL, Eckersley K, Fillery S, Foote KM, Goodwin L, Jones DR, Käck H, Lau A, Nissink JWM, Read J, Scott JS, Taylor B, Walker G, Wissler L, Wylot M. Potent and Selective Inhibitors of MTH1 Probe Its Role in Cancer Cell Survival. J Med Chem 2016; 59:2346-61. [PMID: 26878898 DOI: 10.1021/acs.jmedchem.5b01760] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent literature has claimed that inhibition of the enzyme MTH1 can eradicate cancer. MTH1 is one of the "housekeeping" enzymes that are responsible for hydrolyzing damaged nucleotides in cells and thus prevent them from being incorporated into DNA. We have developed orthogonal and chemically distinct tool compounds to those published in the literature to allow us to test the hypothesis that inhibition of MTH1 has wide applicability in the treatment of cancer. Here we present the work that led to the discovery of three structurally different series of MTH1 inhibitors with excellent potency, selectivity, and proven target engagement in cells. None of these compounds elicited the reported cellular phenotype, and additional siRNA and CRISPR experiments further support these observations. Critically, the difference between the responses of our highly selective inhibitors and published tool compounds suggests that the effect reported for the latter may be due to off-target cytotoxic effects. As a result, we conclude that the role of MTH1 in carcinogenesis and utility of its inhibition is yet to be established.
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Affiliation(s)
- Jason G Kettle
- Oncology Innovative Medicines Unit, AstraZeneca , 35S47 Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom
| | - Husam Alwan
- Oncology Innovative Medicines Unit, AstraZeneca , 35S47 Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom
| | - Michal Bista
- Oncology Innovative Medicines Unit, AstraZeneca , Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
| | - Jason Breed
- Discovery Sciences, AstraZeneca , Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
| | - Nichola L Davies
- Oncology Innovative Medicines Unit, AstraZeneca , Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
| | - Kay Eckersley
- Discovery Sciences, AstraZeneca , Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom
| | - Shaun Fillery
- Oncology Innovative Medicines Unit, AstraZeneca , Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
| | - Kevin M Foote
- Oncology Innovative Medicines Unit, AstraZeneca , Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
| | - Louise Goodwin
- Oncology Innovative Medicines Unit, AstraZeneca , 35S47 Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom
| | - David R Jones
- Oncology Innovative Medicines Unit, AstraZeneca , 35S47 Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom
| | - Helena Käck
- Discovery Sciences, AstraZeneca , Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Alan Lau
- Oncology Innovative Medicines Unit, AstraZeneca , 35S47 Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom
| | - J Willem M Nissink
- Oncology Innovative Medicines Unit, AstraZeneca , Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
| | - Jon Read
- Discovery Sciences, AstraZeneca , Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
| | - James S Scott
- Oncology Innovative Medicines Unit, AstraZeneca , Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
| | - Ben Taylor
- Discovery Sciences, AstraZeneca , Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
| | - Graeme Walker
- Discovery Sciences, AstraZeneca , Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom
| | - Lisa Wissler
- Discovery Sciences, AstraZeneca , Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Marta Wylot
- Oncology Innovative Medicines Unit, AstraZeneca , Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom
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13
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Miller DC, Lunn G, Jones P, Sabnis Y, Davies NL, Driscoll P. Investigation of the effect of molecular properties on the binding kinetics of a ligand to its biological target. Med Chem Commun 2012. [DOI: 10.1039/c2md00270a] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Phillips C, Roberts LR, Schade M, Bazin R, Bent A, Davies NL, Moore R, Pannifer AD, Pickford AR, Prior SH, Read CM, Scott A, Brown DG, Xu B, Irving SL. Design and structure of stapled peptides binding to estrogen receptors. J Am Chem Soc 2011; 133:9696-9. [PMID: 21612236 DOI: 10.1021/ja202946k] [Citation(s) in RCA: 193] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Synthetic peptides that specifically bind nuclear hormone receptors offer an alternative approach to small molecules for the modulation of receptor signaling and subsequent gene expression. Here we describe the design of a series of novel stapled peptides that bind the coactivator peptide site of estrogen receptors. Using a number of biophysical techniques, including crystal structure analysis of receptor-stapled peptide complexes, we describe in detail the molecular interactions and demonstrate that all-hydrocarbon staples modulate molecular recognition events. The findings have implications for the design of stapled peptides in general.
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15
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Bogdan AR, Davies NL, James K. Comparison of diffusion coefficients for matched pairs of macrocyclic and linear molecules over a drug-like molecular weight range. Org Biomol Chem 2011; 9:7727-33. [DOI: 10.1039/c1ob05996c] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Williams DH, Davies NL, Koivisto JJ. Importance of structural tightening, as opposed to partially bound States, in the determination of chemical shift changes at noncovalently bonded interfaces. J Am Chem Soc 2004; 126:14267-72. [PMID: 15506794 DOI: 10.1021/ja047198y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [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
Two models (A and B) have been proposed to account for decreased downfield chemical shifts of a proton bound by noncovalent interactions at a ligand/antibiotic interface as the number of ligand/antibiotic interactions is decreased. In model A, the proton involved in the noncovalent bond suffers a smaller downfield shift because the bond is, with a relatively large probability, broken, and not because it is longer. In model B, the proton involved in the noncovalent bond suffers a smaller downfield shift because the bond is longer, and not because it is, with a relatively large probability, broken. We show that model A cannot account for the chemical shift changes. Model B accounts for the process of positively cooperative binding, in which noncovalent bonds are reduced in length and thereby increase the stability of the organized state.
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17
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Williams DH, Davies NL, Zerella R, Bardsley B. Noncovalent interactions: defining cooperativity. Ligand binding aided by reduced dynamic behavior of receptors. Binding of bacterial cell wall analogues to ristocetin A. J Am Chem Soc 2004; 126:2042-9. [PMID: 14971938 DOI: 10.1021/ja039409p] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [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
Changes in the relative populations of the monomer and asymmetric dimer forms of ristocetin A, upon binding of two molecules of ligand, suggest that ligand binding is negatively cooperative with respect to dimerization. However, strong hydrogen bonds formed in the binding sites of the ligands are reinforced in the dimer relative to the monomer, and the barrier to dissociation of the dimer is increased upon binding of the ligands. It is concluded that the interactions which are common in the binding of both ligands are made with positive cooperativity with respect to those involved in dimerization. The conclusions are relevant to the binding of ligands to proteins, where ligand binding energy can be derived from stabilization of the protein in its ligand-bound form.
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Affiliation(s)
- Dudley H Williams
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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18
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Abstract
Glycopeptide antibiotics of the vancomycin group bind to bacterial cell wall analogue precursors, and typically also form dimers. We have studied the interplay between these two sets of noncovalent bonds formed at separate interfaces. Indole-2-carboxylic acid (L) forms a set of hydrogen bonds to the glycopeptide antibiotic chloroeremomycin (CE) that are analogous to those formed by N-Ac-D-Ala. The ligand/CE dimer interactions (in L/CE/CE/L) are shown to occur with positive cooperativity and structural tightening at the dimer interface. From theoretical considerations and from other data, it is inferred, but not proven, that in the exercise of positive cooperativity, the interface that will be tightened to the greatest degree is the one that lies in the shallowest free energy well.
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Affiliation(s)
- Hideyuki Shiozawa
- Cambridge Center for Molecular Recognition, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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19
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Langley GJ, Herniman JM, Davies NL, Brown T. Simplified sample preparation for the analysis of oligonucleotides by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 1999; 13:1717-1723. [PMID: 10455240 DOI: 10.1002/(sici)1097-0231(19990915)13:17<1717::aid-rcm704>3.0.co;2-r] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS) for the analyses of oligonucleotides has generally been carried out using negative ionisation conditions, usually following ammonium ion-exchange chromatography and the addition of ammonium buffers to the MALDI matrix. The molecular ion region is complex, due to the varying degrees of ammoniation of the phosphate backbone of the oligonucleotide. This gives rise to an overall decrease in sensitivity compared with similar size peptides and can cause ambiguity of assignment of the relative molecular mass of the sample. This study describes the use of H(+) ion exchange resin in situ as the means of removing alkali metal ions from the phosphate backbone of the oligonucleotide. An increase in resolution, sensitivity and identification of the molecular species is reported, with little or no difference in sensitivity observed between positive or negative ionisation spectra. This method is now used for routine screening of synthetic oligonucleotides with a gain in sensitivity of 1-2 orders of magnitude compared with previous methods, and mass assignment errors of +/-0.1% are routinely recorded for externally calibrated data.
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Affiliation(s)
- G J Langley
- Department of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
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20
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Affiliation(s)
- M C Smith
- Newnham Court Veterinary Group, Weavering, Maidstone, Kent
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21
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Davies NL, Williams JH. Emphysematous cystitis in a non-diabetic cat. J S Afr Vet Assoc 1993; 64:162-4. [PMID: 8176696] [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: 01/29/2023] Open
Abstract
Emphysematous cystitis in man and domestic animals is reviewed. A case of emphysematous cystitis occurring 5 d after standard therapy for urethral obstruction in a non-diabetic male Siamese-cross cat is described. Escherichia coli was isolated, and the cystitis resolved after antibiotic therapy.
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Affiliation(s)
- N L Davies
- Department of Companion Animal Medicine and Surgery, Faculty of Veterinary Science, Medical University of Southern Africa, Medunsa, Republic of South Africa
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22
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Davies NL. Lithium toxicity in two dogs. J S Afr Vet Assoc 1991; 62:140-2. [PMID: 1770485] [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: 12/28/2022] Open
Abstract
Two cases of lithium toxicity are reported on in dogs having had lithium hypochlorite chlorinated water as their sole source of drinking water. Clinical signs in one dog included polyuria, polydipsia, loss of body mass; dehydration, diarrhoea and general weakness and in the other case, polyuria, polydipsia, loss of body mass and seizures. Withdrawal of the water resulted in complete recovery.
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Affiliation(s)
- N L Davies
- Department of Companion Animal Medicine and Surgery, Faculty of Veterinary Science, Medical University of Southern Africa, Medunsa
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23
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Davies NL. Complications of ovarian autotransplantation in bitches: an update. J S Afr Vet Assoc 1990; 61:171. [PMID: 9044917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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24
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Davies NL. Complications of ovarian autotransplantation in bitches. J S Afr Vet Assoc 1989; 60:145. [PMID: 2634772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Autotransplantation of the ovary to the portal vein drainage area was performed in 1,130 bitches over a period of 5 years. Complications of this procedure occurred in 41 bitches and included gastric ulceration, recurring pro-oestrus and neoplastic transformation of the transplant.
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Davies NL, Wilson JM. Ultrastructural study of chilling injury in roots of Episcia reptans (Mart.). Planta 1984; 160:185-189. [PMID: 24258423 DOI: 10.1007/bf00392869] [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] [Subscribe] [Scholar Register] [Received: 09/05/1983] [Accepted: 10/09/1983] [Indexed: 06/02/2023]
Abstract
Chilling the roots of the ultra-chill-sensitive plant Episcia reptans at 5-15° C for 1-50 h produced ultrastructural changes such as mitochondrial swelling, tonoplast discontinuity and sub-cellular deposition of two types of crystalline compounds. One deposit, found by pepsin digestion to be proteinaceous, was associated with the tonoplast and its structure changed with time. The other deposit occurred in the cytoplasm, had a non-variable structure and was not digested by pepsin.
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Affiliation(s)
- N L Davies
- School of Plant Biology, University College of North Wales, Deiniol Road, LL57 2UW, Bangor, Gwynedd, UK
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