1
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Lucas SCC, Milbradt AG, Blackwell JH, Bonomo S, Brierley A, Cassar DJ, Freeman J, Hadfield TE, Morrill LA, Riemens R, Sarda S, Schiesser S, Wiktelius D, Ahmed S, Bostock MJ, Börjesson U, De Fusco C, Guerot C, Hargreaves D, Hewitt S, Lamb ML, Su N, Whatling R, Wheeler M, Kettle JG. Design of a Lead-Like Cysteine-Targeting Covalent Library and the Identification of Hits to Cys55 of Bfl-1. J Med Chem 2024. [PMID: 38916990 DOI: 10.1021/acs.jmedchem.4c00781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Covalent hit identification is a viable approach to identify chemical starting points against difficult-to-drug targets. While most researchers screen libraries of <2k electrophilic fragments, focusing on lead-like compounds can be advantageous in terms of finding hits with improved affinity and with a better chance of identifying cryptic pockets. However, due to the increased molecular complexity, larger numbers of compounds (>10k) are desirable to ensure adequate coverage of chemical space. Herein, the approach taken to build a library of 12k covalent lead-like compounds is reported, utilizing legacy compounds, robust library chemistry, and acquisitions. The lead-like covalent library was screened against the antiapoptotic protein Bfl-1, and six promising hits that displaced the BIM peptide from the PPI interface were identified. Intriguingly, X-ray crystallography of lead-like compound 8 showed that it binds to a previously unobserved conformation of the Bfl-1 protein and is an ideal starting point for the optimization of Bfl-1 inhibitors.
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Affiliation(s)
- Simon C C Lucas
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Alexander G Milbradt
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - J Henry Blackwell
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Silvia Bonomo
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Andrew Brierley
- Compound Synthesis and Management, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Doyle J Cassar
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Jared Freeman
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolic Disorders (CVRM), Biopharmaceuticals R&D, AstraZeneca, Gothenburg, SE-43183, Sweden
| | - Thomas E Hadfield
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Lucas A Morrill
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Rick Riemens
- Medicinal Chemistry, Oncology R&D, Acerta B. V., a Part of the AstraZeneca Group, Oss 5349, The Netherlands
| | - Sunil Sarda
- Compound Synthesis and Management, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Stefan Schiesser
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), Biopharmaceuticals R&D, AstraZeneca, Gothenburg, SE-43183, Sweden
| | - Daniel Wiktelius
- Compound Synthesis and Management, Discovery Sciences, R&D, AstraZeneca, Gothenburg, SE-43183, Sweden
| | - Samiyah Ahmed
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Mark J Bostock
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Ulf Börjesson
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Gothenburg, SE-43183, Sweden
| | - Claudia De Fusco
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Carine Guerot
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - David Hargreaves
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Sarah Hewitt
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Michelle L Lamb
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Nancy Su
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Ryan Whatling
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Matthew Wheeler
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Jason G Kettle
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
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2
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Lucas SCC, Ahmed A, Ashraf SN, Argyrou A, Bauer MR, De Donatis GM, Demanze S, Eisele F, Fusani L, Hock A, Kadamur G, Li S, Macmillan-Jones A, Michaelides IN, Phillips C, Rehnström M, Richter M, Rodrigo-Brenni MC, Shilliday F, Wang P, Storer RI. Optimization of Potent Ligands for the E3 Ligase DCAF15 and Evaluation of Their Use in Heterobifunctional Degraders. J Med Chem 2024; 67:5538-5566. [PMID: 38513086 DOI: 10.1021/acs.jmedchem.3c02136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Unlocking novel E3 ligases for use in heterobifunctional PROTAC degraders is of high importance to the pharmaceutical industry. Over-reliance on the current suite of ligands used to recruit E3 ligases could limit the potential of their application. To address this, potent ligands for DCAF15 were optimized using cryo-EM supported, structure-based design to improve on micromolar starting points. A potent binder, compound 24, was identified and subsequently conjugated into PROTACs against multiple targets. Following attempts on degrading a number of proteins using DCAF15 recruiting PROTACs, only degradation of BRD4 was observed. Deconvolution of the mechanism of action showed that this degradation was not mediated by DCAF15, thereby highlighting both the challenges faced when trying to expand the toolbox of validated E3 ligase ligands for use in PROTAC degraders and the pitfalls of using BRD4 as a model substrate.
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Affiliation(s)
- Simon C C Lucas
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Afshan Ahmed
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - S Neha Ashraf
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Argyrides Argyrou
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Matthias R Bauer
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | | | - Sylvain Demanze
- Oncology Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Frederik Eisele
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg SE-431 83,Sweden
| | - Lucia Fusani
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Andreas Hock
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Ganesh Kadamur
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Shuyou Li
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, People's Republic of China
| | | | | | - Christopher Phillips
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Marie Rehnström
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg SE-431 83, Sweden
| | - Magdalena Richter
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Monica C Rodrigo-Brenni
- Safety Innovation and PROTAC Safety, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Fiona Shilliday
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Peng Wang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, People's Republic of China
| | - R Ian Storer
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
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3
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Ghiandoni GM, Evertsson E, Riley DJ, Tyrchan C, Rathi PC. Augmenting DMTA using predictive AI modelling at AstraZeneca. Drug Discov Today 2024; 29:103945. [PMID: 38460568 DOI: 10.1016/j.drudis.2024.103945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 03/11/2024]
Abstract
Design-Make-Test-Analyse (DMTA) is the discovery cycle through which molecules are designed, synthesised, and assayed to produce data that in turn are analysed to inform the next iteration. The process is repeated until viable drug candidates are identified, often requiring many cycles before reaching a sweet spot. The advent of artificial intelligence (AI) and cloud computing presents an opportunity to innovate drug discovery to reduce the number of cycles needed to yield a candidate. Here, we present the Predictive Insight Platform (PIP), a cloud-native modelling platform developed at AstraZeneca. The impact of PIP in each step of DMTA, as well as its architecture, integration, and usage, are discussed and used to provide insights into the future of drug discovery.
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Affiliation(s)
- Gian Marco Ghiandoni
- Augmented DMTA Platform, R&D IT, AstraZeneca, The Discovery Centre (DISC), Francis Crick Avenue, Cambridge CB2 0AA, UK.
| | - Emma Evertsson
- Research and Early Development, Respiratory and Immunology (R&I), Biopharmaceuticals R&D, AstraZeneca, Pepparedsleden, Mölndal, SE 43183, Sweden
| | - David J Riley
- Augmented DMTA Platform, R&D IT, AstraZeneca, The Discovery Centre (DISC), Francis Crick Avenue, Cambridge CB2 0AA, UK
| | - Christian Tyrchan
- Research and Early Development, Respiratory and Immunology (R&I), Biopharmaceuticals R&D, AstraZeneca, Pepparedsleden, Mölndal, SE 43183, Sweden
| | - Prakash Chandra Rathi
- Augmented DMTA Platform, R&D IT, AstraZeneca, The Discovery Centre (DISC), Francis Crick Avenue, Cambridge CB2 0AA, UK
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4
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Engen K, Lundbäck T, Yadav A, Puthiyaparambath S, Rosenström U, Gising J, Jenmalm-Jensen A, Hallberg M, Larhed M. Inhibition of Insulin-Regulated Aminopeptidase by Imidazo [1,5-α]pyridines-Synthesis and Evaluation. Int J Mol Sci 2024; 25:2516. [PMID: 38473764 DOI: 10.3390/ijms25052516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
Inhibition of insulin-regulated aminopeptidase (IRAP) has been shown to improve cognitive functions in several animal models. Recently, we performed a screening campaign of approximately 10,000 compounds, identifying novel small-molecule-based compounds acting as inhibitors of the enzymatic activity of IRAP. Here we report on the chemical synthesis, structure-activity relationships (SAR) and initial characterization of physicochemical properties of a series of 48 imidazo [1,5-α]pyridine-based inhibitors, including delineation of their mode of action as non-competitive inhibitors with a small L-leucine-based IRAP substrate. The best compound displays an IC50 value of 1.0 µM. We elucidate the importance of two chiral sites in these molecules and find they have little impact on the compound's metabolic stability or physicochemical properties. The carbonyl group of a central urea moiety was initially believed to mimic substrate binding to a catalytically important Zn2+ ion in the active site, although the plausibility of this binding hypothesis is challenged by observation of excellent selectivity versus the closely related aminopeptidase N (APN). Taken together with the non-competitive inhibition pattern, we also consider an alternative model of allosteric binding.
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Affiliation(s)
- Karin Engen
- Department of Medicinal Chemistry, Uppsala University, BMC, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Thomas Lundbäck
- Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Division of Chemical Biology and Genome Engineering, Karolinska Institutet, Tomtebodavägen 23A, SE-171 65 Solna, Sweden
- Mechanistic & Structural Biology, Discovery Sciences, R&D, AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Anubha Yadav
- The Beijer Laboratory, Science for Life Laboratory, Department of Medicinal Chemistry, Uppsala University, BMC, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Sharathna Puthiyaparambath
- The Beijer Laboratory, Science for Life Laboratory, Department of Medicinal Chemistry, Uppsala University, BMC, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Ulrika Rosenström
- Department of Medicinal Chemistry, Uppsala University, BMC, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Johan Gising
- The Beijer Laboratory, Science for Life Laboratory, Department of Medicinal Chemistry, Uppsala University, BMC, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Annika Jenmalm-Jensen
- Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Division of Chemical Biology and Genome Engineering, Karolinska Institutet, Tomtebodavägen 23A, SE-171 65 Solna, Sweden
| | - Mathias Hallberg
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Neuropharmacology and Addiction Research, Uppsala University, BMC, P.O. Box 591, SE-751 24 Uppsala, Sweden
| | - Mats Larhed
- The Beijer Laboratory, Science for Life Laboratory, Department of Medicinal Chemistry, Uppsala University, BMC, P.O. Box 574, SE-751 23 Uppsala, Sweden
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5
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Zhao H. Kinetic modelling of the P-glycoprotein mediated efflux with a large-scale matched molecular pair analysis. Eur J Med Chem 2023; 261:115830. [PMID: 37774507 DOI: 10.1016/j.ejmech.2023.115830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/01/2023]
Abstract
P-glycoprotein (Pgp) mediated efflux impacts on the drug absorption, distribution, metabolism and excretion, and confers multidrug resistance to cancer cells. Kinetic modelling provides mechanistic insights into the relationship between the substrate-Pgp interactions and efflux, and bridges the gap between the preference of polar compounds as Pgp substrates and the hydrophobic nature of its drug-binding site. Matched molecular pair analysis supports the guidelines of controlling H-bond donors and polar surface area in the efflux mitigation, but also reveals insufficiency of this type of rule-based approach. Contrary to the rule-of-five compliant compounds, proteolysis-targeting chimeras (PROTACs) have shown the opposite preference of physicochemical properties to evade efflux. Our analysis reiterates the critical role of intrinsic passive permeability in the efflux ratio, and indeed, its mitigation is often driven by increased passive permeability. It is thus useful to separate the passive permeability from the structural context-specific substrate-Pgp interactions in the design cycle.
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Affiliation(s)
- Hongtao Zhao
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
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6
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Perspective on high-throughput bioanalysis to support in vitro assays in early drug discovery. Bioanalysis 2023; 15:177-191. [PMID: 36917553 DOI: 10.4155/bio-2022-0207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
As the desire for a shortened design/make/test/learn cycle increases in early drug discovery, the pressure to rapidly deliver drug metabolism pharmacokinetic data continues to rise. From a bioanalytical standpoint, in vitro assays are challenging because they are amenable to automation and thus capable of generating a high number of samples for analysis. To keep up with analysis demands, automated method development workflows, rapid sample analysis approaches and efficient data analysis software must be utilized. This work provides an outline of how we implemented those three aspects to provide bioanalytical support for in vitro drug metabolism pharmacokinetic assays, which include developing hundreds of mass spectrometry methods and analyzing thousands of samples per week, while delivering a median bioanalytical turnaround time of 1-2 business days.
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7
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Martins V, Fazal L, Oganesian A, Shah A, Stow J, Walton H, Wilsher N. A commentary on the use of pharmacoenhancers in the pharmaceutical industry and the implication for DMPK drug discovery strategies. Xenobiotica 2022; 52:786-796. [PMID: 36537234 DOI: 10.1080/00498254.2022.2130838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Paxlovid, a drug combining nirmatrelvir and ritonavir, was designed for the treatment of COVID-19 and its rapid development has led to emergency use approval by the FDA to reduce the impact of COVID-19 infection on patients.In order to overcome potentially suboptimal therapeutic exposures, nirmatrelvir is dosed in combination with ritonavir to boost the pharmacokinetics of the active product.Here we consider examples of drugs co-administered with pharmacoenhancers.Pharmacoenhancers have been adopted for multiple purposes such as ensuring therapeutic exposure of the active product, reducing formation of toxic metabolites, changing the route of administration, and increasing the cost-effectiveness of a therapy.We weigh the benefits and risks of this approach, examining the impact of technology developments on drug design and how enhanced integration between cross-discipline teams can improve the outcome of drug discovery.
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8
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Begnini F, Geschwindner S, Johansson P, Wissler L, Lewis RJ, Danelius E, Luttens A, Matricon P, Carlsson J, Lenders S, König B, Friedel A, Sjö P, Schiesser S, Kihlberg J. Importance of Binding Site Hydration and Flexibility Revealed When Optimizing a Macrocyclic Inhibitor of the Keap1-Nrf2 Protein-Protein Interaction. J Med Chem 2022; 65:3473-3517. [PMID: 35108001 PMCID: PMC8883477 DOI: 10.1021/acs.jmedchem.1c01975] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Upregulation of the transcription factor Nrf2 by inhibition of the interaction with its negative regulator Keap1 constitutes an opportunity for the treatment of disease caused by oxidative stress. We report a structurally unique series of nanomolar Keap1 inhibitors obtained from a natural product-derived macrocyclic lead. Initial exploration of the structure-activity relationship of the lead, followed by structure-guided optimization, resulted in a 100-fold improvement in inhibitory potency. The macrocyclic core of the nanomolar inhibitors positions three pharmacophore units for productive interactions with key residues of Keap1, including R415, R483, and Y572. Ligand optimization resulted in the displacement of a coordinated water molecule from the Keap1 binding site and a significantly altered thermodynamic profile. In addition, minor reorganizations of R415 and R483 were accompanied by major differences in affinity between ligands. This study therefore indicates the importance of accounting both for the hydration and flexibility of the Keap1 binding site when designing high-affinity ligands.
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Affiliation(s)
- Fabio Begnini
- Department
of Chemistry—BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Stefan Geschwindner
- Mechanistic
and Structural Biology, Discovery Sciences, R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Patrik Johansson
- Mechanistic
and Structural Biology, Discovery Sciences, R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Lisa Wissler
- Mechanistic
and Structural Biology, Discovery Sciences, R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Richard J. Lewis
- Department
of Medicinal Chemistry, Research and Early Development, Respiratory
and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Emma Danelius
- Department
of Chemistry—BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Andreas Luttens
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box
596, 75124 Uppsala, Sweden
| | - Pierre Matricon
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box
596, 75124 Uppsala, Sweden
| | - Jens Carlsson
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box
596, 75124 Uppsala, Sweden
| | - Stijn Lenders
- Department
of Chemistry—BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Beate König
- Department
of Chemistry—BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Anna Friedel
- Department
of Chemistry—BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Peter Sjö
- Drugs
for Neglected Diseases Initiative (DNDi), 15 Chemin Camille-Vidart, 1202 Geneva, Switzerland
| | - Stefan Schiesser
- Department
of Medicinal Chemistry, Research and Early Development, Respiratory
and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, 43183 Mölndal, Sweden,
| | - Jan Kihlberg
- Department
of Chemistry—BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden,
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9
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Measurements of drugs and metabolites in biological matrices using SFC and SFE-SFC-MS. SEP SCI TECHNOL 2022. [DOI: 10.1016/b978-0-323-88487-7.00004-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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10
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Wesche F, De Maria L, Leek T, Narjes F, Bird J, Su W, Czechtizky W. Automated high-throughput in vitro assays to identify metabolic hotspots and protease stability of structurally diverse, pharmacologically active peptides for inhalation. J Pharm Biomed Anal 2021; 211:114518. [DOI: 10.1016/j.jpba.2021.114518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 11/27/2022]
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11
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Schiesser S, Hajek P, Pople HE, Käck H, Öster L, Cox RJ. Discovery and optimization of cyclohexane-1,4-diamines as allosteric MALT1 inhibitors. Eur J Med Chem 2021; 227:113925. [PMID: 34742013 DOI: 10.1016/j.ejmech.2021.113925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 11/19/2022]
Abstract
Inhibition of mucosa-associated lymphoid tissue lymphoma translocation protein-1 (MALT1) is a promising strategy to modulate NF-κB signaling, with the potential to treat B-cell lymphoma and autoimmune diseases. We describe the discovery and optimization of (1s,4s)-N,N'-diaryl cyclohexane-1,4-diamines, a novel series of allosteric MALT1 inhibitors, resulting in compound 8 with single digit micromolar cell potency. X-ray analysis confirms that this compound binds to an induced allosteric site in MALT1. Compound 8 is highly selective and has an excellent in vivo rat PK profile with low clearance and high oral bioavailability, making it a promising lead for further optimization.
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Affiliation(s)
- Stefan Schiesser
- Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden.
| | - Peter Hajek
- Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Huw E Pople
- Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden; School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Helena Käck
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Linda Öster
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Rhona J Cox
- Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
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12
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Wernevik J, Hulthe J, McPheat C, Di Castro S, Lundbäck T. Letter to the Editor: Implementation of Acoustic Dispensing and 384-Well Based Workflows to Improve Assay Capacity and Reduce Compound and Solvent Use in Early Drug Metabolism and Pharmacokinetics Profiling. Assay Drug Dev Technol 2021; 19:410-411. [PMID: 34463123 DOI: 10.1089/adt.2021.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Johan Wernevik
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Johan Hulthe
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Cameron McPheat
- Precision Medicine and Biosamples, Oncology R&D, AstraZeneca, Gothenburg, Sweden
| | - Silvio Di Castro
- Compound Synthesis and Management, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Thomas Lundbäck
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
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13
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Soltani S, Hallaj-Nezhadi S, Rashidi MR. A comprehensive review of in silico approaches for the prediction and modulation of aldehyde oxidase-mediated drug metabolism: The current features, challenges and future perspectives. Eur J Med Chem 2021; 222:113559. [PMID: 34119831 DOI: 10.1016/j.ejmech.2021.113559] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 01/09/2023]
Abstract
The importance of aldehyde oxidase (AOX) in drug metabolism necessitates the development and application of the in silico rational drug design methods as an integral part of drug discovery projects for the early prediction and modulation of AOX-mediated metabolism. The current study represents an up-to-date and thorough review of in silico studies of AOX-mediated metabolism and modulation methods. In addition, the challenges and the knowledge gap that should be covered have been discussed. The importance of aldehyde oxidase (AOX) in drug metabolism is a hot topic in drug discovery. Different strategies are available for the modulation of the AOX-mediated metabolism of drugs. Application of the rational drug design methods as an integral part of drug discovery projects is necessary for the early prediction of AOX-mediated metabolism. The current study represents a comprehensive review of AOX molecular structure, AOX-mediated reactions, AOX substrates, AOX inhibition, approaches to modify AOX-mediated metabolism, prediction of AOX metabolism/substrates/inhibitors, and the AOX related structure-activity relationship (SAR) studies. Furthermore, an up-to-date and thorough review of in silico studies of AOX metabolism has been carried out. In addition, the challenges and the knowledge gap that should be covered in the scientific literature have been discussed in the current review.
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Affiliation(s)
- Somaieh Soltani
- Pharmaceutical Analysis Research Center and Pharmacy Faculty, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Somayeh Hallaj-Nezhadi
- Drug Applied Research Center and Pharmacy Faculty, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Reza Rashidi
- Stem Cell and Regenerative Medicine Institute and Pharmacy faculty, Tabriz University of Medical Sciences, Iran.
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14
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Nissink JWM, Bazzaz S, Blackett C, Clark MA, Collingwood O, Disch JS, Gikunju D, Goldberg K, Guilinger JP, Hardaker E, Hennessy EJ, Jetson R, Keefe AD, McCoull W, McMurray L, Olszewski A, Overman R, Pflug A, Preston M, Rawlins PB, Rivers E, Schimpl M, Smith P, Truman C, Underwood E, Warwicker J, Winter-Holt J, Woodcock S, Zhang Y. Generating Selective Leads for Mer Kinase Inhibitors-Example of a Comprehensive Lead-Generation Strategy. J Med Chem 2021; 64:3165-3184. [PMID: 33683117 DOI: 10.1021/acs.jmedchem.0c01904] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mer is a member of the TAM (Tyro3, Axl, Mer) kinase family that has been associated with cancer progression, metastasis, and drug resistance. Their essential function in immune homeostasis has prompted an interest in their role as modulators of antitumor immune response in the tumor microenvironment. Here we illustrate the outcomes of an extensive lead-generation campaign for identification of Mer inhibitors, focusing on the results from concurrent, orthogonal high-throughput screening approaches. Data mining, HT (high-throughput), and DECL (DNA-encoded chemical library) screens offered means to evaluate large numbers of compounds. We discuss campaign strategy and screening outcomes, and exemplify series resulting from prioritization of hits that were identified. Concurrent execution of HT and DECL screening successfully yielded a large number of potent, selective, and novel starting points, covering a range of selectivity profiles across the TAM family members and modes of kinase binding, and offered excellent start points for lead development.
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Affiliation(s)
| | - Sana Bazzaz
- X-Chem, Inc., Waltham, Massachusetts 02453, United States
| | - Carolyn Blackett
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | | | | | - Jeremy S Disch
- X-Chem, Inc., Waltham, Massachusetts 02453, United States
| | - Diana Gikunju
- X-Chem, Inc., Waltham, Massachusetts 02453, United States
| | | | | | | | - Edward J Hennessy
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Rachael Jetson
- X-Chem, Inc., Waltham, Massachusetts 02453, United States
| | | | - William McCoull
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | | | | | - Ross Overman
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Alexander Pflug
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Marian Preston
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Philip B Rawlins
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Emma Rivers
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Marianne Schimpl
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Paul Smith
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Caroline Truman
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | | | - Juli Warwicker
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Jon Winter-Holt
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Simon Woodcock
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Ying Zhang
- X-Chem, Inc., Waltham, Massachusetts 02453, United States
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15
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Begnini F, Poongavanam V, Over B, Castaldo M, Geschwindner S, Johansson P, Tyagi M, Tyrchan C, Wissler L, Sjö P, Schiesser S, Kihlberg J. Mining Natural Products for Macrocycles to Drug Difficult Targets. J Med Chem 2020; 64:1054-1072. [PMID: 33337880 PMCID: PMC7872424 DOI: 10.1021/acs.jmedchem.0c01569] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
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Lead
generation for difficult-to-drug targets that have large,
featureless, and highly lipophilic or highly polar and/or flexible
binding sites is highly challenging. Here, we describe how cores of
macrocyclic natural products can serve as a high-quality in
silico screening library that provides leads for difficult-to-drug
targets. Two iterative rounds of docking of a carefully selected set
of natural-product-derived cores led to the discovery of an uncharged
macrocyclic inhibitor of the Keap1-Nrf2 protein–protein interaction,
a particularly challenging target due to its highly polar binding
site. The inhibitor displays cellular efficacy and is well-positioned
for further optimization based on the structure of its complex with
Keap1 and synthetic access. We believe that our work will spur interest
in using macrocyclic cores for in silico-based lead
generation and also inspire the design of future macrocycle screening
collections.
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Affiliation(s)
- Fabio Begnini
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | | | - Björn Over
- Department of Medicinal Chemistry, Research and Early Development, Early Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Marie Castaldo
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Stefan Geschwindner
- Structure, Biophysics & Fragment-Based Lead Generation, Discovery Sciences, R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Patrik Johansson
- Structure, Biophysics & Fragment-Based Lead Generation, Discovery Sciences, R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Mohit Tyagi
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Christian Tyrchan
- Department of Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Lisa Wissler
- Structure, Biophysics & Fragment-Based Lead Generation, Discovery Sciences, R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Peter Sjö
- Drugs for Neglected Diseases initiative (DNDi), 15 Chemin Louis Dunant, 1202 Geneva, Switzerland
| | - Stefan Schiesser
- Department of Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
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16
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Schiesser S, Chepliaka H, Kollback J, Quennesson T, Czechtizky W, Cox RJ. N-Trifluoromethyl Amines and Azoles: An Underexplored Functional Group in the Medicinal Chemist’s Toolbox. J Med Chem 2020; 63:13076-13089. [DOI: 10.1021/acs.jmedchem.0c01457] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Stefan Schiesser
- Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Hanna Chepliaka
- Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
- Department of Chemistry, Ludwig-Maximilians Universität München, Butenandstrasse 5−13, 81377 Munich, Germany
| | - Johanna Kollback
- Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
- Department of Chemistry and Molecular Biology, Göteborgs universitet, Kemigården 4, 41296 Gothenburg, Sweden
| | - Thibaut Quennesson
- Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
- Université de Lille, Institut Pasteur de Lille, INSERM U1177 − Drugs and Molecules for Living Systems, 59000 Lille, France
| | - Werngard Czechtizky
- Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Rhona J. Cox
- Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
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17
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Kanebratt KP, Janefeldt A, Vilén L, Vildhede A, Samuelsson K, Milton L, Björkbom A, Persson M, Leandersson C, Andersson TB, Hilgendorf C. Primary Human Hepatocyte Spheroid Model as a 3D In Vitro Platform for Metabolism Studies. J Pharm Sci 2020; 110:422-431. [PMID: 33122050 DOI: 10.1016/j.xphs.2020.10.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/19/2020] [Accepted: 10/19/2020] [Indexed: 12/12/2022]
Abstract
3D cultures of primary human hepatocytes (PHH) are emerging as a more in vivo-like culture system than previously available hepatic models. This work describes the characterisation of drug metabolism in 3D PHH spheroids. Spheroids were formed from three different donors of PHH and the expression and activities of important cytochrome P450 enzymes (CYP1A2, 2B6, 2C9, 2D6, and 3A4) were maintained for up to 21 days after seeding. The activity of CYP2B6 and 3A4 decreased, while the activity of CYP2C9 and 2D6 increased over time (P < 0.05). For six test compounds, that are metabolised by multiple enzymes, intrinsic clearance (CLint) values were comparable to standard in vitro hepatic models and successfully predicted in vivo CLint within 3-fold from observed values for low clearance compounds. Remarkably, the metabolic turnover of these low clearance compounds was reproducibly measured using only 1-3 spheroids, each composed of 2000 cells. Importantly, metabolites identified in the spheroid cultures reproduced the major metabolites observed in vivo, both primary and secondary metabolites were captured. In summary, the 3D PHH spheroid model shows promise to be used in drug discovery projects to study drug metabolism, including unknown mechanisms, over an extended period of time.
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Affiliation(s)
- Kajsa P Kanebratt
- DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden.
| | - Annika Janefeldt
- DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden
| | - Liisa Vilén
- DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden
| | - Anna Vildhede
- DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden
| | - Kristin Samuelsson
- DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden
| | - Lucas Milton
- DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden
| | - Anders Björkbom
- DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden
| | - Marie Persson
- DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden
| | - Carina Leandersson
- Physical & Analytical Chemistry, Research and Early Development Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden
| | - Tommy B Andersson
- DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden
| | - Constanze Hilgendorf
- DMPK, Research and Early Development Cardiovascular Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca Gothenburg, Sweden
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18
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Green CP, Spencer PA, Sarda S. Advancing automation in Compound Management: a novel industrial process underpinning drug discovery. Drug Discov Today 2020; 26:5-9. [PMID: 33031945 DOI: 10.1016/j.drudis.2020.09.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/08/2020] [Accepted: 09/28/2020] [Indexed: 11/29/2022]
Abstract
Faced with ageing infrastructure and ever-increasing demands from hit discovery and lead optimisation functions, AstraZeneca has chosen to develop innovative technologies and process solutions to support the future of drug discovery. These include the miniaturisation of compound storage tubes for high-density storage and rapid access to the corporate collection for feeding samples to the predicted tripling number of high throughput screening (HTS) campaigns. The acoustically- compatible tubes also enable the first fully-acoustic plate production process for faster sample supply to screening with less waste and continued high quality. Operating at a smaller scale reduces compound synthesis, storage, and consumption, prompting miniaturisation of upstream chemistry and downstream biological assays, while offering a transformative and sustainable solution to many drug discovery issues applicable across the industry.
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Affiliation(s)
- Clive P Green
- Sample Management, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Philip A Spencer
- Sample Management, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Sunil Sarda
- Sample Management, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.
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