1
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Wang S, Liang D, Wang J, Dong K, Zhang Y, Liang H, Xu X, Song T. FraHMT: A Fragment-Oriented Heterogeneous Graph Molecular Generation Model for Target Proteins. J Chem Inf Model 2024; 64:3718-3732. [PMID: 38644797 DOI: 10.1021/acs.jcim.4c00252] [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: 04/23/2024]
Abstract
The molecular generation task stands as a pivotal step in the domains of computational chemistry and drug discovery, aiming to computationally generate molecular structures for specific properties. In contrast to previous models that focused primarily on SMILES strings or molecular graphs, our model placed a special emphasis on the substructure information on molecules, enabling the model to learn richer chemical rules and structure features from fragments and chemical reaction information on molecules. To accomplish this, we fragmented the molecules to construct heterogeneous graph representations based on atom and fragment information. Then our model mapped the heterogeneous graph data into a latent vector space by using an encoder and employed a self-regressive generative model as a decoder for molecular generation. Additionally, we performed transfer learning on the model using a small set of ligand molecules known to be active against the target protein to generate molecules that bind better to the target protein. Experimental results demonstrate that our model is highly competitive with state-of-the-art models. It can generate valid and diverse molecules with favorable physicochemical properties and drug-likeness. Importantly, they produce novel molecules with high docking scores against the target proteins.
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Affiliation(s)
- Shuang Wang
- College of Computer Science and Technology, China University of Petroleum, QingDao 266580, China
| | - Dingming Liang
- College of Computer Science and Technology, China University of Petroleum, QingDao 266580, China
| | - Jianmin Wang
- College of Computer Science and Technology, China University of Petroleum, QingDao 266580, China
- The Interdisciplinary Graduate Program in Integrative Biotechnology, Yonsei University, Incheon 21983, Republic of Korea
| | - Kaiyu Dong
- College of Computer Science and Technology, China University of Petroleum, QingDao 266580, China
| | - Yunjing Zhang
- College of Computer Science and Technology, China University of Petroleum, QingDao 266580, China
| | - Huicong Liang
- Marine Biomedical Institute of Qingdao, School of Medicine and Pharmacy, Ocean University of China, QingDao 266580, China
| | - Ximing Xu
- Marine Biomedical Institute of Qingdao, School of Medicine and Pharmacy, Ocean University of China, QingDao 266580, China
| | - Tao Song
- College of Computer Science and Technology, China University of Petroleum, QingDao 266580, China
- Department of Artificial Intelligence, Faculty of Computer Science, Polytechnical University of Madrid, Madrid 28031, Spain
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2
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van Vlijmen H, Pannifer AD, Cochrane P, Basting D, Li VM, Engkvist O, Ortholand JY, Wagener M, Duffy J, Finsinger D, Davis J, van Helden SP, de Vlieger JSB. The European Lead Factory: Results from a decade of collaborative, public-private, drug discovery programs. Drug Discov Today 2024; 29:103886. [PMID: 38244673 DOI: 10.1016/j.drudis.2024.103886] [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: 10/31/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 01/22/2024]
Abstract
The European Lead Factory (ELF) is a consortium of universities and small and medium-sized enterprises (SMEs) dedicated to drug discovery, and the pharmaceutical industry. This unprecedented consortium provides high-throughput screening, triage, and hit validation, including to non-consortium members. The ELF library was created through a novel compound-sharing model between nine pharmaceutical companies and expanded through library synthesis by chemistry-specialized SMEs. The library has been screened against ∼270 different targets and 15 phenotypic assays, and hits have been developed to form the basis of patents and spin-off companies. Here, we review the outcome of screening campaigns of the ELF, including the performance and physicochemical properties of the library, identification of possible frequent hitter compounds, and the effectiveness of the compound-sharing model.
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Affiliation(s)
| | | | | | | | - Volkhart M Li
- Bayer AG, Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Ola Engkvist
- AstraZeneca Discovery Sciences, Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | | | | | - James Duffy
- Medicines for Malaria Venture, ICC 20, Rte de Pré-Bois, 1215 Geneva, Switzerland
| | - Dirk Finsinger
- Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Jeremy Davis
- UCB Biopharma UK, 216 Bath Road, Slough, SL1 3WE, UK
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3
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Barnes L, Birkinshaw TN, Senior AJ, Brügge OS, Lewis W, Argent SP, Moody CJ, Nortcliffe A. Iodoetherification as a strategy towards sp 3-rich scaffolds for drug discovery. Bioorg Med Chem 2024; 101:117636. [PMID: 38354458 DOI: 10.1016/j.bmc.2024.117636] [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: 12/13/2023] [Revised: 01/30/2024] [Accepted: 02/07/2024] [Indexed: 02/16/2024]
Abstract
Functionalised tetrahydropyran and spirooxepane scaffolds were prepared utilising an iodoetherification strategy and elaborated to demonstrate their potential use in library synthesis. The iodoetherification products could be readily transformed to the corresponding azides that could be further functionalised via copper-catalysed azide-alkyne cycloaddition or reduction to the amine. The lead-likeness and three-dimensionality of the scaffolds were examined and compared to commercial libraries.
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Affiliation(s)
- Lydia Barnes
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Timothy N Birkinshaw
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Aaron J Senior
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Oscar Siles Brügge
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - William Lewis
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Stephen P Argent
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Christopher J Moody
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Andrew Nortcliffe
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom.
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4
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Werner E, Wiegand M, Moran J, Lebœuf D. Rapid Access to Densely Functionalized Cyclopentenyl Sulfoximines through a Sc-Catalyzed Aza-Piancatelli Reaction. Org Lett 2024. [PMID: 38190622 DOI: 10.1021/acs.orglett.3c04095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Sulfoximines make up a class of compounds of growing interest for crop science and medicinal chemistry, but methods for directly incorporating them into complex molecular scaffolds are lacking. Here we report a scandium-catalyzed variant of the aza-Piancatelli cyclization that can directly incorporate sulfoximines as nucleophiles rather than the classical aniline substrates. Starting from 2-furylcarbinols and sulfoximines, the reaction provides direct access to 4-sulfoximinocyclopentenones, a new scaffold bearing cyclopentenone and sulfoximine motifs, both of interest for bioactive compounds.
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Affiliation(s)
- Emilie Werner
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg, 8 Allée Gaspard Monge, 67000 Strasbourg, France
| | - Milena Wiegand
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg, 8 Allée Gaspard Monge, 67000 Strasbourg, France
| | - Joseph Moran
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg, 8 Allée Gaspard Monge, 67000 Strasbourg, France
- Institut Universitaire de France (IUF), 75005 Paris, France
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - David Lebœuf
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg, 8 Allée Gaspard Monge, 67000 Strasbourg, France
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5
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Beng TK, Garcia J, Eichwald J, Borg C. Introducing a sulfone-embedded anhydride to the anhydride-imine reaction for the modular synthesis of N-heterocyclic sulfones bearing vicinal stereocenters. RSC Adv 2023; 13:14355-14360. [PMID: 37180005 PMCID: PMC10171042 DOI: 10.1039/d3ra01812a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023] Open
Abstract
N-heterocyclic sulfones constitute the core of several pharmaceuticals, including the antityrpanosomal drug Nifurtimox. Their biological relevance and architectural complexity makes them valued targets and inspires the development of more selective and atom-economical strategies for their construction and post-modification. In this embodiment, we describe a flexible approach to sp3-rich N-heterocyclic sulfones, which hinges on the efficient annulation of a novel sulfone-embedded anhydride with 1,3-azadienes and aryl aldimines. Further elaboration of the lactam esters has facilitated the construction of a library of vicinally functionalized sulfone-embedded N-heterocycles.
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Affiliation(s)
- Timothy K Beng
- Department of Chemistry, Central Washington University Ellensburg WA 98926 USA
| | - Jorge Garcia
- Department of Chemistry, Central Washington University Ellensburg WA 98926 USA
| | - Jane Eichwald
- Department of Chemistry, Central Washington University Ellensburg WA 98926 USA
| | - Claire Borg
- Department of Chemistry, Central Washington University Ellensburg WA 98926 USA
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6
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Okolo EA, Pahl A, Sievers S, Pask CM, Nelson A, Marsden SP. Scaffold Remodelling of Diazaspirotricycles Enables Synthesis of Diverse sp 3 -Rich Compounds With Distinct Phenotypic Effects. Chemistry 2023; 29:e202203992. [PMID: 36722618 PMCID: PMC10946999 DOI: 10.1002/chem.202203992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/02/2023]
Abstract
A 'top down' scaffold remodelling approach to library synthesis was applied to spirotricyclic ureas prepared by a complexity-generating oxidative dearomatisation. Eighteen structurally-distinct, sp3 -rich scaffolds were accessed from the parent tricycle through ring addition, cleavage and expansion strategies. Biological screening of a small compound library based on these scaffolds using the cell-painting assay demonstrated distinctive phenotypic responses engendered by different library members, illustrating the functional as well as structural diversity of the compounds.
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Affiliation(s)
| | - Axel Pahl
- Max-Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 11Dortmund44227Germany
| | - Sonja Sievers
- Max-Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 11Dortmund44227Germany
| | | | - Adam Nelson
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
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7
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Janin YL. On drug discovery against infectious diseases and academic medicinal chemistry contributions. Beilstein J Org Chem 2022; 18:1355-1378. [PMID: 36247982 PMCID: PMC9531561 DOI: 10.3762/bjoc.18.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/21/2022] [Indexed: 11/23/2022] Open
Abstract
This perspective is an attempt to document the problems that medicinal chemists are facing in drug discovery. It is also trying to identify relevant/possible, research areas in which academics can have an impact and should thus be the subject of grant calls. Accordingly, it describes how hit discovery happens, how compounds to be screened are selected from available chemicals and the possible reasons for the recurrent paucity of useful/exploitable results reported. This is followed by the successful hit to lead stories leading to recent and original antibacterials which are, or about to be, used in human medicine. Then, illustrated considerations and suggestions are made on the possible inputs of academic medicinal chemists. This starts with the observation that discovering a "good" hit in the course of a screening campaign still rely on a lot of luck - which is within the reach of academics -, that the hit to lead process requires a lot of chemistry and that if public-private partnerships can be important throughout these stages, they are absolute requirements for clinical trials. Concerning suggestions to improve the current hit success rate, one academic input in organic chemistry would be to identify new and pertinent chemical space, design synthetic accesses to reach these and prepare the corresponding chemical libraries. Concerning hit to lead programs on a given target, if no new hits are available, previously reported leads along with new structural data can be pertinent starting points to design, prepare and assay original analogues. In conclusion, this text is an actual plea illustrating that, in many countries, academic research in medicinal chemistry should be more funded, especially in the therapeutic area neglected by the industry. At the least, such funds would provide the intensive to secure series of hopefully relevant chemical entities which appears to often lack when considering the results of academic as well as industrial screening campaigns.
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Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
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8
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Knez D, Gobec S, Hrast M. Screening of Big Pharma’s Library against Various in-house Biological Targets. Molecules 2022; 27:molecules27144484. [PMID: 35889355 PMCID: PMC9320114 DOI: 10.3390/molecules27144484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/27/2022] [Accepted: 07/08/2022] [Indexed: 12/04/2022] Open
Abstract
Open innovation initiatives provide opportunities for collaboration and sharing of knowledge and experience between industry, academia, and government institutions. Through open innovation, Merck is offering a Mini Library of 80 carefully selected compounds from previous research and development projects to a broader scientific community for testing in academic drug discovery projects. These compounds are predominantly drug-like and cover a broad range of molecular targets. They could potentially interact with other enzymes, receptors, transporters, and ion channels of interest. The Mini Library was tested on seven in-house enzymes (bacterial MurA, MurC ligase, and DdlB enzyme, human MAO-A/B, human BChE, and murine AChE), and several hits were identified. A follow-up series of structural analogues provided by Merck gave a more detailed insight into the accessibility and the quality of the hit compounds. For example, sartan derivatives were moderate inhibitors of MurC, whereas bisarylureas were potent, selective, nanomolar inhibitors of hMAO-B. Importantly, 3-n-butyl-substituted indoles were identified as low nanomolar selective inhibitors of hBChE. All in all, the hit derivatives provide new starting points for the further exploration of the chemical space of high-quality enzyme inhibitors.
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9
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Silvestri IP, Colbon PJJ. The Growing Importance of Chirality in 3D Chemical Space Exploration and Modern Drug Discovery Approaches for Hit-ID: Topical Innovations. ACS Med Chem Lett 2021; 12:1220-1229. [PMID: 34413951 PMCID: PMC8366003 DOI: 10.1021/acsmedchemlett.1c00251] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/02/2021] [Indexed: 12/19/2022] Open
Abstract
Modern-day drug discovery is now blessed with a wide range of high-throughput hit identification (hit-ID) strategies that have been successfully validated in recent years, with particular success coming from high-throughput screening, fragment-based lead discovery, and DNA-encoded library screening. As screening efficiency and throughput increases, this enables the viable exploration of increasingly complex three-dimensional (3D) chemical structure space, with a realistic chance of identifying highly specific hit ligands with increased target specificity and reduced attrition rates in preclinical and clinical development. This minireview will explore the impact of an improved design of multifunctionalized, sp3-rich, stereodefined scaffolds on the (virtual) exploration of 3D chemical space and the specific requirements for different hit-ID technologies.
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Affiliation(s)
- Ilaria Proietti Silvestri
- Department of Chemistry University
of Liverpool, Liverpool ChiroChem, Ltd., Crown Street, Liverpool L69 7ZD, United
Kingdom
| | - Paul J. J. Colbon
- Department of Chemistry University
of Liverpool, Liverpool ChiroChem, Ltd., Crown Street, Liverpool L69 7ZD, United
Kingdom
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10
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Lach D, Zhdan U, Smolinski A, Polanski J. Functional and Material Properties in Nanocatalyst Design: A Data Handling and Sharing Problem. Int J Mol Sci 2021; 22:ijms22105176. [PMID: 34068386 PMCID: PMC8153597 DOI: 10.3390/ijms22105176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 11/16/2022] Open
Abstract
(1) Background: Properties and descriptors are two forms of molecular in silico representations. Properties can be further divided into functional, e.g., catalyst or drug activity, and material, e.g., X-ray crystal data. Millions of real measured functional property records are available for drugs or drug candidates in online databases. In contrast, there is not a single database that registers a real conversion, TON or TOF data for catalysts. All of the data are molecular descriptors or material properties, which are mainly of a calculation origin. (2) Results: Here, we explain the reason for this. We reviewed the data handling and sharing problems in the design and discovery of catalyst candidates particularly, material informatics and catalyst design, structural coding, data collection and validation, infrastructure for catalyst design and the online databases for catalyst design. (3) Conclusions: Material design requires a property prediction step. This can only be achieved based on the registered real property measurement. In reality, in catalyst design and discovery, we can observe either a severe functional property deficit or even property famine.
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Affiliation(s)
- Daniel Lach
- Institute of Chemistry, Faculty of Science and Technology, University of Silesia, Szkolna 9, 40-006 Katowice, Poland; (D.L.); (U.Z.)
| | - Uladzislau Zhdan
- Institute of Chemistry, Faculty of Science and Technology, University of Silesia, Szkolna 9, 40-006 Katowice, Poland; (D.L.); (U.Z.)
| | - Adam Smolinski
- Central Mining Institute, Plac Gwarkow 1, 40-166 Katowice, Poland;
| | - Jaroslaw Polanski
- Institute of Chemistry, Faculty of Science and Technology, University of Silesia, Szkolna 9, 40-006 Katowice, Poland; (D.L.); (U.Z.)
- Correspondence: ; Tel.: +48-32-259-9978
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11
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van Vlijmen H, Ortholand JY, Li VMJ, de Vlieger JSB. The European Lead Factory: An updated HTS compound library for innovative drug discovery. Drug Discov Today 2021; 26:2406-2413. [PMID: 33892142 DOI: 10.1016/j.drudis.2021.04.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 04/07/2021] [Accepted: 04/12/2021] [Indexed: 11/16/2022]
Abstract
Through the European Lead Factory model, industry-standard high-throughput screening and hit validation are made available to academia, small and medium-sized enterprises, charity organizations, patient foundations, and participating pharmaceutical companies. The compound collection used for screening is built from a unique diversity of sources. It brings together compounds from companies with different therapeutic area heritages and completely new compounds from library synthesis. This generates structural diversity and combines molecules with complementary physicochemical properties. In 2019, the screening library was updated to enable another 5 years of running innovative drug discovery projects. Here, we investigate the physicochemical and diversity properties of the updated compound collection. We show that it is highly diverse, drug-like, and complementary to commercial screening libraries.
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Affiliation(s)
- Herman van Vlijmen
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium.
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12
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Nelson A, Karageorgis G. Natural product-informed exploration of chemical space to enable bioactive molecular discovery. RSC Med Chem 2021; 12:353-362. [PMID: 34046620 PMCID: PMC8130614 DOI: 10.1039/d0md00376j] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/08/2020] [Indexed: 12/27/2022] Open
Abstract
The search for new bioactive molecules remains an open challenge limiting our ability to discover new drugs to treat disease and chemical probes to comprehensively study biological processes. The vastness of chemical space renders its exploration unfeasible by synthesis alone. Historically, chemists have tended to explore chemical space unevenly without committing to systematic frameworks for navigation. This minireview covers a range of approaches that take inspiration from the structure or origin of natural products, and help focus molecular discovery on biologically-relevant regions of chemical space. All these approaches have enabled the discovery of distinctive and novel bioactive small molecules such as useful chemical probes of biological mechanisms. This minireview comments on how such approaches may be developed into more general frameworks for the systematic identification of currently unexplored regions of biologically-relevant chemical space, a challenge that is central to both chemical biology and medicinal chemistry.
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Affiliation(s)
- Adam Nelson
- School of Chemistry, University of Leeds Woodhouse Lane LS2 9JT UK
- Astbury Centre for Structural and Molecular Biology, University of Leeds Woodhouse Lane LS2 9JT UK
| | - George Karageorgis
- School of Chemistry, University of Leeds Woodhouse Lane LS2 9JT UK
- Astbury Centre for Structural and Molecular Biology, University of Leeds Woodhouse Lane LS2 9JT UK
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13
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Davis AM, Engkvist O, Fairclough RJ, Feierberg I, Freeman A, Iyer P. Public-Private Partnerships: Compound and Data Sharing in Drug Discovery and Development. SLAS DISCOVERY 2021; 26:604-619. [PMID: 33586501 DOI: 10.1177/2472555220982268] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Collaborative efforts between public and private entities such as academic institutions, governments, and pharmaceutical companies form an integral part of scientific research, and notable instances of such initiatives have been created within the life science community. Several examples of alliances exist with the broad goal of collaborating toward scientific advancement and improved public welfare. Such collaborations can be essential in catalyzing breaking areas of science within high-risk or global public health strategies that may have otherwise not progressed. A common term used to describe these alliances is public-private partnership (PPP). This review discusses different aspects of such partnerships in drug discovery/development and provides example applications as well as successful case studies. Specific areas that are covered include PPPs for sharing compounds at various phases of the drug discovery process-from compound collections for hit identification to sharing clinical candidates. Instances of PPPs to support better data integration and build better machine learning models are also discussed. The review also provides examples of PPPs that address the gap in knowledge or resources among involved parties and advance drug discovery, especially in disease areas with unfulfilled and/or social needs, like neurological disorders, cancer, and neglected and rare diseases.
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Affiliation(s)
- Andrew M Davis
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Ola Engkvist
- Molecular AI, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Rebecca J Fairclough
- Emerging Innovations Unit, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Isabella Feierberg
- Molecular AI, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Boston, USA
| | - Adrian Freeman
- Emerging Innovations Unit, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Preeti Iyer
- Molecular AI, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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14
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Abstract
It is well established that medicinal chemists should depart from the flat, sp2-dominated nature of traditional drugs and incorporate complexities of bioactive natural products, such as sp3-richness, 3D topology and chirality. There is a gray area, however, in the relevance of newly developed chemical scaffolds that exhibit these complexities but do not correlate to anything observed in nature. This can leave synthetic methodologists searching for structural similarities between their newly developed products and known natural products in search of justification. This article offers a perspective on how these types of complex 'abiotic' scaffolds can be appreciated purely on the basis of their structural novelty, and identifies the unique advantages arising when a complex chemical entity unrecognized by nature is introduced to biological systems.
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15
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Synthesis of sp3-rich chemical libraries based upon 1,2-diazetidines. Tetrahedron 2021. [DOI: 10.1016/j.tet.2020.131836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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16
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Ramsden JI, Cosgrove SC, Turner NJ. Is it time for biocatalysis in fragment-based drug discovery? Chem Sci 2020; 11:11104-11112. [PMID: 34094353 PMCID: PMC8162304 DOI: 10.1039/d0sc04103c] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/07/2020] [Indexed: 12/26/2022] Open
Abstract
The use of biocatalysts for fragment-based drug discovery has yet to be fully investigated, despite the promise enzymes hold for the synthesis of poly-functional, non-protected small molecules. Here we analyze products of the biocatalysis literature to demonstrate the potential for not only fragment generation, but also the enzyme-mediated elaboration of these fragments. Our analysis demonstrates that biocatalytic products can readily populate 3D chemical space, offering diverse catalytic approaches to help generate new, bioactive molecules.
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Affiliation(s)
- Jeremy I Ramsden
- Department of Chemistry, Manchester Institute of Biotechnology, University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Sebastian C Cosgrove
- Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, University of Manchester 131 Princess Street Manchester M1 7DN UK
- School of Chemical and Physical Science, Lennard-Jones Laboratories, Keele University Staffordshire ST5 5BG UK
| | - Nicholas J Turner
- Department of Chemistry, Manchester Institute of Biotechnology, University of Manchester 131 Princess Street Manchester M1 7DN UK
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17
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Le T, Winter R, Noé F, Clevert DA. Neuraldecipher - reverse-engineering extended-connectivity fingerprints (ECFPs) to their molecular structures. Chem Sci 2020; 11:10378-10389. [PMID: 34094299 PMCID: PMC8162443 DOI: 10.1039/d0sc03115a] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/10/2020] [Indexed: 12/22/2022] Open
Abstract
Protecting molecular structures from disclosure against external parties is of great relevance for industrial and private associations, such as pharmaceutical companies. Within the framework of external collaborations, it is common to exchange datasets by encoding the molecular structures into descriptors. Molecular fingerprints such as the extended-connectivity fingerprints (ECFPs) are frequently used for such an exchange, because they typically perform well on quantitative structure-activity relationship tasks. ECFPs are often considered to be non-invertible due to the way they are computed. In this paper, we present a fast reverse-engineering method to deduce the molecular structure given revealed ECFPs. Our method includes the Neuraldecipher, a neural network model that predicts a compact vector representation of compounds, given ECFPs. We then utilize another pre-trained model to retrieve the molecular structure as SMILES representation. We demonstrate that our method is able to reconstruct molecular structures to some extent, and improves, when ECFPs with larger fingerprint sizes are revealed. For example, given ECFP count vectors of length 4096, we are able to correctly deduce up to 69% of molecular structures on a validation set (112 K unique samples) with our method.
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Affiliation(s)
- Tuan Le
- Department of Digital Technologies, Bayer AG Berlin Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin Berlin Germany
| | - Robin Winter
- Department of Digital Technologies, Bayer AG Berlin Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin Berlin Germany
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin Berlin Germany
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18
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Honarnejad S, van Boeckel S, van den Hurk H, van Helden S. Hit Discovery for Public Target Programs in the European Lead Factory: Experiences and Output from Assay Development and Ultra-High-Throughput Screening. SLAS DISCOVERY 2020; 26:192-204. [PMID: 32734803 PMCID: PMC8637381 DOI: 10.1177/2472555220942765] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The European Lead Factory (ELF) consortium provides European academics and small and medium enterprises access to ~0.5 million unique compounds, a state-of-the-art ultra-high-throughput screening (u-HTS) platform, and industrial early drug discovery (DD) expertise with the aim of delivering innovative DD starting points. From 2013 to 2018, 154 proposals for eight target classes in seven therapeutic areas were submitted to the ELF consortium, 88 of which were accepted by the selection committee. During this period, 76 primary assays based on seven different readout technologies were optimized and mainly miniaturized to 1536-well plates. In total, 72 u-HTS campaigns were carried out, and follow-up work including hit triage through orthogonal, deselection, selectivity, and biophysical assays were finalized. This ambitious project showed that besides the quality of the compound library and the primary assay, the success of centralized u-HTS of large compound libraries across many target classes, various assay types, and different readout technologies is also largely dependent on the capacity and flexibility of the automation on one hand and the hit-triaging phase on the other, particularly because of undesired compound-assay interference. Thus far, the delivered hit lists from the ELF consortium have resulted in spinoffs, patents, in vivo proof of concepts, preclinical development programs, peer-reviewed publications, PhD theses, and much more, demonstrating early success indications.
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Affiliation(s)
- Saman Honarnejad
- Pivot Park Screening Centre B.V., Oss, North Brabant, The Netherlands
| | - Stan van Boeckel
- Pivot Park Screening Centre B.V., Oss, North Brabant, The Netherlands
| | | | - Steven van Helden
- Pivot Park Screening Centre B.V., Oss, North Brabant, The Netherlands
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19
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Ishigami-Yuasa M, Kagechika H. Chemical Screening of Nuclear Receptor Modulators. Int J Mol Sci 2020; 21:E5512. [PMID: 32752136 PMCID: PMC7432305 DOI: 10.3390/ijms21155512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/24/2020] [Accepted: 07/28/2020] [Indexed: 12/15/2022] Open
Abstract
Nuclear receptors are ligand-inducible transcriptional factors that control multiple biological phenomena, including proliferation, differentiation, reproduction, metabolism, and the maintenance of homeostasis. Members of the nuclear receptor superfamily have marked structural and functional similarities, and their domain functionalities and regulatory mechanisms have been well studied. Various modulators of nuclear receptors, including agonists and antagonists, have been developed as tools for elucidating nuclear receptor functions and also as drug candidates or lead compounds. Many assay systems are currently available to evaluate the modulation of nuclear receptor functions, and are useful as screening tools in the discovery and development of new modulators. In this review, we cover the chemical screening methods for nuclear receptor modulators, focusing on assay methods and chemical libraries for screening. We include some recent examples of the discovery of nuclear receptor modulators.
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Affiliation(s)
| | - Hiroyuki Kagechika
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan;
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20
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Dean C, Rajkumar S, Roesner S, Carson N, Clarkson GJ, Wills M, Jones M, Shipman M. Readily accessible sp 3-rich cyclic hydrazine frameworks exploiting nitrogen fluxionality. Chem Sci 2020; 11:1636-1642. [PMID: 32206282 PMCID: PMC7069508 DOI: 10.1039/c9sc04849a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/23/2019] [Indexed: 12/12/2022] Open
Abstract
Increased molecular complexity correlates with improved chances of success in the drug development process. Here, a strategy for the creation of sp3-rich, non-planar heterocyclic scaffolds suitable for drug discovery is described that obviates the need to generate multiple stereogenic centers with independent control. Asymmetric transfer hydrogenation using a tethered Ru-catalyst is used to efficiently produce a range of enantiopure cyclic hydrazine building blocks (up to 99% ee). Iterative C-N functionalization at the two nitrogen atoms of these compounds produces novel hydrazine and hydrazide based chemical libraries. Wide chemical diversification is possible through variation in the hydrazine structure, use of different functionalization chemistries and coupling partners, and controlled engagement of each nitrogen of the hydrazine in turn. Principal Moment of Inertia (PMI) analysis of this small hydrazine library reveals excellent shape diversity and three-dimensionality. NMR and crystallographic studies confirm these frameworks prefer to orient their substituents in three-dimensional space under the control of a single stereogenic center through exploitation of the fluxional behavior of the two nitrogen atoms.
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Affiliation(s)
- Conor Dean
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
| | - Sundaram Rajkumar
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
| | - Stefan Roesner
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
| | - Nessa Carson
- AMRI UK, Ltd. , Erl Wood Manor , Windlesham , Surrey GU20 6PH , UK
| | - Guy J Clarkson
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
| | - Martin Wills
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
| | - Matthew Jones
- Eli Lilly & Company Ltd. , Erl Wood Manor , Windlesham , Surrey GU20 6PH , UK
| | - Michael Shipman
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
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21
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Miyakawa S, Okui T, Shiraishi T, Yoshihara T, Hirayama M, Satomi Y, Hamada T, Nishida M, Akimoto C, Sato S. Development of novel highly sensitive methods to detect endogenous cGAMP in cells and tissue. J Immunol Methods 2020; 480:112751. [PMID: 31982420 DOI: 10.1016/j.jim.2020.112751] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 12/26/2019] [Accepted: 01/21/2020] [Indexed: 11/29/2022]
Abstract
Intracellular DNA triggers interferon release during the innate immune response. Cyclic GMP-AMP synthase (cGAS) senses intracellular double-stranded DNA not only in response to viral infection but also under autoimmune conditions. Measuring the levels of cyclic GMP-AMP (cGAMP) as a second messenger of cGAS activation is important to elucidate the physiological and pathological roles of cGAS. Therefore, we generated monoclonal antibodies against cGAMP using hybridoma technology to test antibody specificity and establish methods to detect intracellular cGAMP. The resulting cGAMP-specific antibody enabled the development of a time-resolved fluorescence energy transfer assay with a quantifiable range of 0.1 nM to 100 nM cGAMP. Using this assay, we detected cellular and tissue cGAMP. We confirmed that the cGAMP antibody successfully targeted intracellular cGAMP through immunocytochemical analyses. These results demonstrated that the cGAMP antibody is a powerful tool that allows determining cGAS involvement in autoimmunity and disease pathology at the cell and tissue levels.
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Affiliation(s)
- Shuuichi Miyakawa
- Bio Molecular Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.
| | - Toshitake Okui
- Immunology Unit, Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Tsubasa Shiraishi
- Immunology Unit, Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.
| | - Tomoki Yoshihara
- Bio Molecular Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.
| | - Megumi Hirayama
- Integrated Technology Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan.
| | - Yoshinori Satomi
- Integrated Technology Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan.
| | - Teruki Hamada
- Drug Metabolism & Pharmacokinetics Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.
| | - Mayumi Nishida
- Integrated Technology Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan.
| | - Chihiro Akimoto
- Immunology Unit, Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.
| | - Shuji Sato
- Immunology Unit, Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.
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22
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Wang GW, Boyd O, Young TA, Bertrand SM, Bower JF. Rhodacyclopentanones as Linchpins for the Atom Economical Assembly of Diverse Polyheterocycles. J Am Chem Soc 2020; 142:1740-1745. [DOI: 10.1021/jacs.9b12421] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Gang-Wei Wang
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Olivia Boyd
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Tom A. Young
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Sophie M. Bertrand
- GlaxoSmithKline R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - John F. Bower
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
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23
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Suzuki T, Mate NA, Adhikari AA, Chisholm JD. Dialkylation of Indoles with Trichloroacetimidates to Access 3,3-Disubstituted Indolenines. Molecules 2019; 24:molecules24224143. [PMID: 31731742 PMCID: PMC6891773 DOI: 10.3390/molecules24224143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 12/02/2022] Open
Abstract
2-Substituted indoles may be directly transformed to 3,3-dialkyl indolenines with trichloroacetimidate electrophiles and the Lewis acid TMSOTf. These reactions provide rapid access to complex indolenines which are present in a variety of complex natural products and medicinally relevant small molecule structures. This method provides an alternative to the use of transition metal catalysis. The indolenines are readily transformed into spiroindoline systems which are privileged scaffolds in medicinal chemistry.
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24
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Rice S, Cox DJ, Marsden SP, Nelson A. Unified synthesis of diverse building blocks for application in the discovery of bioactive small molecules. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.130513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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25
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Bunally SB, Luscombe CN, Young RJ. Using Physicochemical Measurements to Influence Better Compound Design. SLAS DISCOVERY 2019; 24:791-801. [PMID: 31429385 DOI: 10.1177/2472555219859845] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
During the past decade, the physicochemical quality of molecules under investigation at all stages of the drug discovery process has come under particular scrutiny. The issues associated with excessive lipophilicity and poor solubility in particular are many and varied, ranging from poor outcomes in screening campaigns to promiscuity, limited and/or poorly predictable pharmacokinetic exposure, and, ultimately, greater chances of clinical failure. In this review, contemporary methods to secure key measurements are described along with their relevance to understanding the behavior of molecules in environments pertinent to pharmacological activity. Together, the various measurements contribute to predictive models of both the physicochemical properties themselves and the outcomes they influence.
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Affiliation(s)
| | | | - Robert J Young
- 1 GlaxoSmithKline Medicines Research Centre, Stevenage, UK
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26
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Kelley AM, Minerali E, Wilent JE, Chambers NJ, Stingley KJ, Wilson GT, Petersen KS. Asymmetric synthesis of novel spirocycles via a chiral phosphoric acid catalyzed desymmetrization. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.03.074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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27
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Volochnyuk DM, Ryabukhin SV, Moroz YS, Savych O, Chuprina A, Horvath D, Zabolotna Y, Varnek A, Judd DB. Evolution of commercially available compounds for HTS. Drug Discov Today 2019; 24:390-402. [DOI: 10.1016/j.drudis.2018.10.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/02/2018] [Accepted: 10/30/2018] [Indexed: 12/17/2022]
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28
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Charon J, Manteca A, Innis CA. Using the Bacterial Ribosome as a Discovery Platform for Peptide-Based Antibiotics. Biochemistry 2019; 58:75-84. [PMID: 30372045 PMCID: PMC7615898 DOI: 10.1021/acs.biochem.8b00927] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The threat of bacteria resistant to multiple antibiotics poses a major public health problem requiring immediate and coordinated action worldwide. While infectious pathogens have become increasingly resistant to commercially available drugs, antibiotic discovery programs in major pharmaceutical companies have produced no new antibiotic scaffolds in 40 years. As a result, new strategies must be sought to obtain a steady supply of novel scaffolds capable of countering the spread of resistance. The bacterial ribosome is a major target for antimicrobials and is inhibited by more than half of the antibiotics used today. Recent studies showing that the ribosome is a target for several classes of ribosomally synthesized antimicrobial peptides point to ribosome-targeting peptides as a promising source of antibiotic scaffolds. In this Perspective, we revisit the current paradigm of antibiotic discovery by proposing that the bacterial ribosome can be used both as a target and as a tool for the production and selection of peptide-based antimicrobials. Turning the ribosome into a high-throughput platform for the directed evolution of peptide-based antibiotics could be achieved in different ways. One possibility would be to use a combination of state-of-the-art microfluidics and genetic reprogramming techniques, which we will review briefly. If it is successful, this strategy has the potential to produce new classes of antibiotics for treating multi-drug-resistant pathogens.
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Affiliation(s)
- Justine Charon
- Institut Européen de Chimie et Biologie, Univ. Bordeaux, Institut National de la Santé et de la Recherche Médicale (U1212) and Centre National de la Recherche Scientifique (UMR 5320), Pessac 33607, France
| | - Aitor Manteca
- Institut Européen de Chimie et Biologie, Univ. Bordeaux, Institut National de la Santé et de la Recherche Médicale (U1212) and Centre National de la Recherche Scientifique (UMR 5320), Pessac 33607, France
| | - C. Axel Innis
- Institut Européen de Chimie et Biologie, Univ. Bordeaux, Institut National de la Santé et de la Recherche Médicale (U1212) and Centre National de la Recherche Scientifique (UMR 5320), Pessac 33607, France
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29
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Flagstad T, Azevedo CMG, Troelsen NS, Min GK, Macé Y, Willaume A, Guilleux R, Velay M, Bonnet K, Morgentin R, Nielsen TE, Clausen MH. Generation of a Heteropolycyclic and sp3
-Rich Scaffold for Library Synthesis from a Highly Diastereoselective Petasis/Diels-Alder and ROM-RCM Reaction Sequence. European J Org Chem 2018. [DOI: 10.1002/ejoc.201801551] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Thomas Flagstad
- Center for Nanomedicine & Theranostics; Department of Chemistry; Technical University of Denmark; Kemitorvet 207 DK-2800 Kongens Lyngby Denmark
| | - Carlos M. G. Azevedo
- Center for Nanomedicine & Theranostics; Department of Chemistry; Technical University of Denmark; Kemitorvet 207 DK-2800 Kongens Lyngby Denmark
| | - Nikolaj S. Troelsen
- Center for Nanomedicine & Theranostics; Department of Chemistry; Technical University of Denmark; Kemitorvet 207 DK-2800 Kongens Lyngby Denmark
| | - Geanna K. Min
- Center for Nanomedicine & Theranostics; Department of Chemistry; Technical University of Denmark; Kemitorvet 207 DK-2800 Kongens Lyngby Denmark
| | - Yohan Macé
- EDELRIS; 115 Avenue Lacassagne F-69003 France
| | | | | | | | | | | | - Thomas E. Nielsen
- Singapore Centre on Environmental Life Science Engineering; Nanyang Technological University; 637551 Singapore Singapore
- Costerton Biofilm Center; Department of Immunology and Microbiology; University of Copenhagen; DK-2200 Copenhagen DK Denmark
| | - Mads H. Clausen
- Center for Nanomedicine & Theranostics; Department of Chemistry; Technical University of Denmark; Kemitorvet 207 DK-2800 Kongens Lyngby Denmark
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30
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An approach towards enhancement of a screening library: The Next Generation Library Initiative (NGLI) at Bayer - against all odds? Drug Discov Today 2018; 24:668-672. [PMID: 30562586 DOI: 10.1016/j.drudis.2018.12.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/26/2018] [Accepted: 12/07/2018] [Indexed: 11/22/2022]
Abstract
Pharmaceutical companies often refer to 'screening their library' when performing high-throughput screening (HTS) on a corporate compound collection to identify lead structures for small-molecule drug discovery programs. Characteristics of such a library, including the size, chemical space covered, and physicochemical properties, often determine the success of a screening campaign. Therefore, strategies to maintain and enhance the overall quality of screening collections are crucial to stay competitive and to cope with the 'novelty erosion' that is observed gradually. The Next Generation Library Initiative (NGLI), the enhancement of Bayer's HTS collection by 500000 newly designed compounds within 5 years, is addressing exactly this challenge. Here, we describe this collaborative project, which involves all internal medicinal chemists in a crowd-sourcing approach, as well as selected external partners, to reach this ambitious goal.
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31
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Morgentin R, Dow M, Aimon A, Karageorgis G, Kalliokoski T, Roche D, Marsden S, Nelson A. Translation of innovative chemistry into screening libraries: an exemplar partnership from the European Lead Factory. Drug Discov Today 2018; 23:1578-1583. [DOI: 10.1016/j.drudis.2018.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 03/29/2018] [Accepted: 05/02/2018] [Indexed: 11/28/2022]
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32
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Boström J, Brown DG, Young RJ, Keserü GM. Expanding the medicinal chemistry synthetic toolbox. Nat Rev Drug Discov 2018; 17:709-727. [DOI: 10.1038/nrd.2018.116] [Citation(s) in RCA: 267] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Wales SM, Adcock HV, Lewis W, Hamza D, Moody CJ. Nitrogen-Bridged, Natural Product Like Octahydrobenzofurans and Octahydroindoles: Scope and Mechanism of Bridge-Forming Reductive Amination via Caged Heteroadamantanes. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800962] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Steven. M. Wales
- School of Chemistry, University Park; University of Nottingham; 2RD Nottingham, NG7 United Kingdom
| | - Holly V. Adcock
- Biocity; Sygnature Discovery Ltd; Pennyfoot Street Nottingham, NG1 1GF United Kingdom
| | - William Lewis
- School of Chemistry, University Park; University of Nottingham; 2RD Nottingham, NG7 United Kingdom
| | - Daniel Hamza
- Biocity; Sygnature Discovery Ltd; Pennyfoot Street Nottingham, NG1 1GF United Kingdom
| | - Christopher J. Moody
- School of Chemistry, University Park; University of Nottingham; 2RD Nottingham, NG7 United Kingdom
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34
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35
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Sato T, Yuki H, Ogura K, Honma T. Construction of an integrated database for hERG blocking small molecules. PLoS One 2018; 13:e0199348. [PMID: 29979714 PMCID: PMC6034787 DOI: 10.1371/journal.pone.0199348] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/06/2018] [Indexed: 11/19/2022] Open
Abstract
The inhibition of the hERG potassium channel is closely related to the prolonged QT interval, and thus assessing this risk could greatly facilitate the development of therapeutic compounds and the withdrawal of hazardous marketed drugs. The recent increase in SAR information about hERG inhibitors in public databases has led to many successful applications of machine learning techniques to predict hERG inhibition. However, most of these reports constructed their prediction models based on only one SAR database because the differences in the data format and ontology hindered the integration of the databases. In this study, we curated the hERG-related data in ChEMBL, PubChem, GOSTAR, and hERGCentral, and integrated them into the largest database about hERG inhibition by small molecules. Assessment of structural diversity using Murcko frameworks revealed that the integrated database contains more than twice as many chemical scaffolds for hERG inhibitors than any of the individual databases, and covers 18.2% of the Murcko framework-based chemical space occupied by the compounds in ChEMBL. The database provides the most comprehensive information about hERG inhibitors and will be useful to design safer compounds for drug discovery. The database is freely available at http://drugdesign.riken.jp/hERGdb/.
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Affiliation(s)
- Tomohiro Sato
- Center for Life Science Technologies, RIKEN, Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, Japan
| | - Hitomi Yuki
- Center for Life Science Technologies, RIKEN, Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, Japan
| | - Keiji Ogura
- Center for Life Science Technologies, RIKEN, Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, Japan
| | - Teruki Honma
- Center for Life Science Technologies, RIKEN, Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, Japan
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36
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Flagstad T, Azevedo CMG, Min G, Willaume A, Morgentin R, Nielsen TE, Clausen MH. Petasis/Diels-Alder/Cyclization Cascade Reactions for the Generation of Scaffolds with Multiple Stereogenic Centers and Orthogonal Handles for Library Production. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800565] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Thomas Flagstad
- Department of Chemistry; Technical University of Denmark; 2800 Kgs. Lyngby Denmark
- Center for Nanomedicine and Theranostics; Technical University of Denmark; 2800 Kgs. Lyngby Denmark
| | - Carlos M. G. Azevedo
- Department of Chemistry; Technical University of Denmark; 2800 Kgs. Lyngby Denmark
- Center for Nanomedicine and Theranostics; Technical University of Denmark; 2800 Kgs. Lyngby Denmark
| | - Geanna Min
- Department of Chemistry; Technical University of Denmark; 2800 Kgs. Lyngby Denmark
- Center for Nanomedicine and Theranostics; Technical University of Denmark; 2800 Kgs. Lyngby Denmark
| | | | | | - Thomas E. Nielsen
- Department of Chemistry; Technical University of Denmark; 2800 Kgs. Lyngby Denmark
- Singapore Centre on Environmental Life Science Engineering; Nanyang Technological University; 637551 Singapore Singapore
- Costerton Biofilm Center; Department of Immunology and Microbiology; University of Copenhagen; 2200 Copenhagen DK- Denmark
| | - Mads H. Clausen
- Department of Chemistry; Technical University of Denmark; 2800 Kgs. Lyngby Denmark
- Center for Nanomedicine and Theranostics; Technical University of Denmark; 2800 Kgs. Lyngby Denmark
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37
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Borst MLG, Ouairy CMJ, Fokkema SC, Cecchi A, Kerckhoffs JMCA, de Boer VL, van den Boogaard PJ, Bus RF, Ebens R, van der Hulst R, Knol J, Libbers R, Lion ZM, Settels BW, de Wever E, Attia KA, Sinnema PJ, de Gooijer JM, Harkema K, Hazewinkel M, Snijder S, Pouwer K. Polycyclic Sulfoximines as New Scaffolds for Drug Discovery. ACS COMBINATORIAL SCIENCE 2018; 20:335-343. [PMID: 29714998 DOI: 10.1021/acscombsci.7b00150] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The design and synthesis of three novel polycyclic scaffolds containing sulfoximines are presented in this work, which exemplify that sulfoximines represent a real opportunity for the discovery of new drug candidates. Additionally, the structures present at least two points of diversification and contain a high level of sp3-character, hence being very interesting 3D scaffolds. The compounds synthesized were added to the compound collection of the European Lead Factory.
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Affiliation(s)
| | | | | | | | | | | | | | - Rutger F. Bus
- Syncom B.V., Kadijk 3, 9747 AT Groningen, The Netherlands
| | - Rijko Ebens
- Syncom B.V., Kadijk 3, 9747 AT Groningen, The Netherlands
| | | | - Joop Knol
- Syncom B.V., Kadijk 3, 9747 AT Groningen, The Netherlands
| | - Rob Libbers
- Syncom B.V., Kadijk 3, 9747 AT Groningen, The Netherlands
| | - Zhou M. Lion
- Syncom B.V., Kadijk 3, 9747 AT Groningen, The Netherlands
| | | | - Ellen de Wever
- Syncom B.V., Kadijk 3, 9747 AT Groningen, The Netherlands
| | | | | | | | - Karen Harkema
- Syncom B.V., Kadijk 3, 9747 AT Groningen, The Netherlands
| | | | - Susan Snijder
- Syncom B.V., Kadijk 3, 9747 AT Groningen, The Netherlands
| | - Kees Pouwer
- Syncom B.V., Kadijk 3, 9747 AT Groningen, The Netherlands
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38
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Liddon JTR, Rossi-Ashton JA, Taylor RJK, Unsworth WP. Dearomatizing Spiroannulation Reagents: Direct Access to Spirocycles from Indoles and Dihalides. Org Lett 2018; 20:3349-3353. [PMID: 29745671 DOI: 10.1021/acs.orglett.8b01248] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Unfunctionalized indoles can be directly converted into 3,3'-spirocyclic indolenines and indolines upon reaction with electrophilic dihalides in the presence of t-BuOK/BEt3. This double C-C bond forming reaction, which simultaneously generates a quaternary spirocyclic center, typically proceeds in high yield and has good functional group tolerance. In contrast to existing dearomatizing spirocyclization approaches, there is no need to prepare a prefunctionalized aromatic precursor, enabling faster access to valuable spirocyclic products from simple, commercially available aromatics in one step.
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Affiliation(s)
- John T R Liddon
- Department of Chemistry , University of York , Heslington , York YO10 5DD , U.K
| | | | - Richard J K Taylor
- Department of Chemistry , University of York , Heslington , York YO10 5DD , U.K
| | - William P Unsworth
- Department of Chemistry , University of York , Heslington , York YO10 5DD , U.K
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39
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Valeur E, Jimonet P. New Modalities, Technologies, and Partnerships in Probe and Lead Generation: Enabling a Mode-of-Action Centric Paradigm. J Med Chem 2018; 61:9004-9029. [DOI: 10.1021/acs.jmedchem.8b00378] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Eric Valeur
- Medicinal Chemistry, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal 431 83, Sweden
| | - Patrick Jimonet
- External Innovation Drug Discovery, Global Business Development & Licensing, Sanofi, 13 quai Jules Guesde, 94400 Vitry-sur-Seine, France
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40
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Volpe R, Lepage RJ, White JM, Krenske EH, Flynn BL. Asymmetric synthesis of multiple quaternary stereocentre-containing cyclopentyls by oxazolidinone-promoted Nazarov cyclizations. Chem Sci 2018; 9:4644-4649. [PMID: 29899958 PMCID: PMC5969496 DOI: 10.1039/c8sc00031j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/19/2018] [Indexed: 01/29/2023] Open
Abstract
Carbometalation of oxazolidinone (Ox)-substituted ynamides is used to generate highly substituted Ox-divinyl (and aryl vinyl) ketones for use in Nazarov cyclizations. The Ox-group serves as a remarkably effective chiral activating group, enabling the torquoselective Nazarov cyclization of these sterically congested substrates to be performed under mild conditions. It also serves as a charge-stabilizing group in the intermediate oxyallyl cation, suppressing undesired [1,2]-sigmatropic shifts of neighboring substituents and facilitating the regio- and stereoselective incorporation of nucleophiles to yield cyclopentanoids containing up to three contiguous all-carbon quaternary (4°) stereocentres.
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Affiliation(s)
- Rohan Volpe
- Monash Institute of Pharmaceutical Sciences , Monash University , 381 Royal Parade , Parkville , Victoria 3052 , Australia .
| | - Romain J Lepage
- School of Chemistry and Molecular Biosciences , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Jonathan M White
- Bio21 Institute , School of Chemistry , University of Melbourne , Parkville , VIC 3010 , Australia
| | - Elizabeth H Krenske
- School of Chemistry and Molecular Biosciences , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Bernard L Flynn
- Monash Institute of Pharmaceutical Sciences , Monash University , 381 Royal Parade , Parkville , Victoria 3052 , Australia .
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41
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Wales SM, Merisor EG, Adcock HV, Pearce CA, Strutt IR, Lewis W, Hamza D, Moody CJ. Diastereoselective Synthesis of Highly Substituted, Amino- and Pyrrolidino-Tetrahydrofurans as Lead-Like Molecular Scaffolds. Chemistry 2018; 24:8233-8239. [DOI: 10.1002/chem.201801046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Steven M. Wales
- School of Chemistry; University Park; University of Nottingham; Nottingham NG7 2RD United Kingdom
| | - Elena G. Merisor
- Sygnature Discovery Ltd, Biocity; Pennyfoot Street Nottingham NG1 1GF United Kingdom
| | - Holly V. Adcock
- Sygnature Discovery Ltd, Biocity; Pennyfoot Street Nottingham NG1 1GF United Kingdom
| | - Christopher A. Pearce
- Sygnature Discovery Ltd, Biocity; Pennyfoot Street Nottingham NG1 1GF United Kingdom
| | - Ian R. Strutt
- Sygnature Discovery Ltd, Biocity; Pennyfoot Street Nottingham NG1 1GF United Kingdom
| | - William Lewis
- School of Chemistry; University Park; University of Nottingham; Nottingham NG7 2RD United Kingdom
| | - Daniel Hamza
- Sygnature Discovery Ltd, Biocity; Pennyfoot Street Nottingham NG1 1GF United Kingdom
| | - Christopher J. Moody
- School of Chemistry; University Park; University of Nottingham; Nottingham NG7 2RD United Kingdom
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42
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Schuhmacher A, Gassmann O, McCracken N, Hinder M. Open innovation and external sources of innovation. An opportunity to fuel the R&D pipeline and enhance decision making? J Transl Med 2018; 16:119. [PMID: 29739427 PMCID: PMC5941640 DOI: 10.1186/s12967-018-1499-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/30/2018] [Indexed: 12/28/2022] Open
Abstract
Historically, research and development (R&D) in the pharmaceutical sector has predominantly been an in-house activity. To enable investments for game changing late-stage assets and to enable better and less costly go/no-go decisions, most companies have employed a fail early paradigm through the implementation of clinical proof-of-concept organizations. To fuel their pipelines, some pioneers started to complement their internal R&D efforts through collaborations as early as the 1990s. In recent years, multiple extrinsic and intrinsic factors induced an opening for external sources of innovation and resulted in new models for open innovation, such as open sourcing, crowdsourcing, public–private partnerships, innovations centres, and the virtualization of R&D. Three factors seem to determine the breadth and depth regarding how companies approach external innovation: (1) the company’s legacy, (2) the company’s willingness and ability to take risks and (3) the company’s need to control IP and competitors. In addition, these factors often constitute the major hurdles to effectively leveraging external opportunities and assets. Conscious and differential choices of the R&D and business models for different companies and different divisions in the same company seem to best allow a company to fully exploit the potential of both internal and external innovations.
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Affiliation(s)
| | - Oliver Gassmann
- Institute for Technology Management, University of St. Gallen, Dufourstrasse 40a, 9000, St. Gallen, Switzerland
| | - Nigel McCracken
- Debiopharm International S.A., Chemin Messidor 5-7, 1002, Lausanne, Switzerland
| | - Markus Hinder
- Novartis Institutes for BioMedical Research, Postfach, Forum 1, 4002, Basel, Switzerland
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43
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Patil P, Mishra B, Sheombarsing G, Kurpiewska K, Kalinowska-Tłuścik J, Dömling A. Library-to-Library Synthesis of Highly Substituted α-Aminomethyl Tetrazoles via Ugi Reaction. ACS COMBINATORIAL SCIENCE 2018; 20:70-74. [PMID: 29215263 PMCID: PMC5813278 DOI: 10.1021/acscombsci.7b00137] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/21/2017] [Indexed: 12/26/2022]
Abstract
α-Aminomethyl tetrazoles, recently made accessible by an Ugi multicomponent reaction (MCR), were shown to be excellent starting materials for a further Ugi MCR, yielding substituted N-methyl-2-(((1-methyl-1H-tetrazol-5-yl)methyl)amino)acetamides having four points of diversity in a library-to-library approach. The scope and limitations of the two-step sequence was explored by conducting more than 50 reactions. Irrespective of electron-rich and electron-deficient oxo-components and the nature of the isocyanide component, the reactions give excellent yields. Sterically less hindered α-aminomethyl tetrazoles give better yields of in further Ugi MCR. The target scaffold has four points of diversity and is finding applications to fill screening decks for high-throughput screening (HTS) in the European Lead Factory and in structure-based drug design.
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Affiliation(s)
- Pravin Patil
- University
of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Bhupendra Mishra
- University
of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Gitanjali Sheombarsing
- University
of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Jagiellonian
University, Faculty of Chemistry, Department
of Crystal Chemistry and Crystal Physics, Biocrystallography Group, Ingardena 3, 30-060 Kraków, Poland
| | - Justyna Kalinowska-Tłuścik
- Jagiellonian
University, Faculty of Chemistry, Department
of Crystal Chemistry and Crystal Physics, Biocrystallography Group, Ingardena 3, 30-060 Kraków, Poland
| | - Alexander Dömling
- University
of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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44
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Geary GC, Nortcliffe A, Pearce CA, Hamza D, Jones G, Moody CJ. Densely functionalised spirocyclic oxetane-piperidine scaffolds for drug discovery. Bioorg Med Chem 2018; 26:791-797. [DOI: 10.1016/j.bmc.2017.12.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/05/2017] [Accepted: 12/07/2017] [Indexed: 10/18/2022]
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45
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Firth JD, Craven PGE, Lilburn M, Pahl A, Marsden SP, Nelson A. A biosynthesis-inspired approach to over twenty diverse natural product-like scaffolds. Chem Commun (Camb) 2018; 52:9837-40. [PMID: 27424656 DOI: 10.1039/c6cc04662b] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A synthetic approach to diverse scaffolds was developed that was inspired by diterpene biosynthesis. Initial scaffolds, generated using Diels-Alder reactions of furyl-functionalised amines, were transformed into alternative scaffolds using cleavage, ring expansion, annulation and rearrangement reactions. In total, 25 diverse scaffolds were prepared that were shown to have high natural product-likeness.
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Affiliation(s)
- James D Firth
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK.
| | | | - Matthew Lilburn
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK.
| | - Axel Pahl
- Max Planck Institute of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
| | | | - Adam Nelson
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK. and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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46
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Aimon A, Karageorgis G, Masters J, Dow M, Craven PGE, Ohsten M, Willaume A, Morgentin R, Ruiz-Llamas N, Lemoine H, Kalliokoski T, Eatherton AJ, Foley DJ, Marsden SP, Nelson A. Realisation of small molecule libraries based on frameworks distantly related to natural products. Org Biomol Chem 2018; 16:3160-3167. [DOI: 10.1039/c8ob00688a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Design and synthesis of compound libraries with focused molecular properties, based on NP-like scaffolds.
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Affiliation(s)
- Anthony Aimon
- School of Chemistry
- University of Leeds
- Leeds LS2 9JT
- UK
| | - George Karageorgis
- School of Chemistry
- University of Leeds
- Leeds LS2 9JT
- UK
- Astbury Centre for Structural Molecular Biology
| | - Jacob Masters
- School of Chemistry
- University of Leeds
- Leeds LS2 9JT
- UK
- Astbury Centre for Structural Molecular Biology
| | - Mark Dow
- School of Chemistry
- University of Leeds
- Leeds LS2 9JT
- UK
| | | | | | | | | | | | | | | | | | - Daniel J. Foley
- School of Chemistry
- University of Leeds
- Leeds LS2 9JT
- UK
- Astbury Centre for Structural Molecular Biology
| | | | - Adam Nelson
- School of Chemistry
- University of Leeds
- Leeds LS2 9JT
- UK
- Astbury Centre for Structural Molecular Biology
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47
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Janssen GV, van den Heuvel JA, Megens RP, Benningshof JC, Ovaa H. Microwave-assisted diastereoselective two-step three-component synthesis for rapid access to drug-like libraries of substituted 3-amino-β-lactams. Bioorg Med Chem 2018; 26:41-49. [DOI: 10.1016/j.bmc.2017.11.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/03/2017] [Accepted: 11/08/2017] [Indexed: 01/12/2023]
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48
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Narhe BD, Breman AC, Padwal J, Vandenput DA, Scheidt JM, Benningshof JC, van der Marel GA, Overkleeft HS, van der Stelt M, Filippov DV. Piperidine and octahydropyrano[3,4-c] pyridine scaffolds for drug-like molecular libraries of the European Lead Factory. Bioorg Med Chem 2017; 25:5160-5170. [DOI: 10.1016/j.bmc.2017.07.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/06/2017] [Accepted: 07/07/2017] [Indexed: 11/26/2022]
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49
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Vishwanatha TM, Kurpiewska K, Kalinowska-Tłuścik J, Dömling A. Cysteine Isocyanide in Multicomponent Reaction: Synthesis of Peptido-Mimetic 1,3-Azoles. J Org Chem 2017; 82:9585-9594. [PMID: 28817272 PMCID: PMC5603900 DOI: 10.1021/acs.joc.7b01615] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
An alternative approach toward the
simple and robust synthesis
of highly substituted peptidic thiazole derivatives using Ugi-multicomponent
reaction (U-MCR) is described. Thus, we introduced the enantiopure
(R)-2-methyl-2-isocyano-3-(tritylthio)propanoate
as a novel class of isocyanide in MCR. This bifunctional isocyanide
was found to undergo mild cyclodehydration to afford thiazole containing
peptidomimetics in a short synthetic sequence. Several examples of
bis-heterocyclic rings were also synthesized through the proper choice
of the aldehyde component in the U-4CR. The method opens a wide range
of applications toward the synthesis of nonribosomal natural products
and other bioactive compounds.
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Affiliation(s)
- Thimmalapura M Vishwanatha
- University of Groningen , Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Jagiellonian University , Department of Crystal Chemistry and Crystal Physics, Ingardena 3, 30-060 Krakow, Poland
| | - Justyna Kalinowska-Tłuścik
- Jagiellonian University , Department of Crystal Chemistry and Crystal Physics, Ingardena 3, 30-060 Krakow, Poland
| | - Alexander Dömling
- University of Groningen , Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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50
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Nicolle SM, Nortcliffe A, Bartrum HE, Lewis W, Hayes CJ, Moody CJ. C−H Insertion as a Key Step to Spiro-Oxetanes, Scaffolds for Drug Discovery. Chemistry 2017; 23:13623-13627. [DOI: 10.1002/chem.201703746] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Simon M. Nicolle
- School of Chemistry; University of Nottingham; University Park Nottingham NG7 2RD United Kingdom
| | - Andrew Nortcliffe
- School of Chemistry; University of Nottingham; University Park Nottingham NG7 2RD United Kingdom
| | - Hannah E. Bartrum
- School of Chemistry; University of Nottingham; University Park Nottingham NG7 2RD United Kingdom
| | - William Lewis
- School of Chemistry; University of Nottingham; University Park Nottingham NG7 2RD United Kingdom
| | - Christopher J. Hayes
- School of Chemistry; University of Nottingham; University Park Nottingham NG7 2RD United Kingdom
| | - Christopher J. Moody
- School of Chemistry; University of Nottingham; University Park Nottingham NG7 2RD United Kingdom
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