1
|
Carmo RLL, Galster SL, Wdowik T, Song C, Chemler SR. Copper-Catalyzed Enantioselective Aerobic Alkene Aminooxygenation and Dioxygenation: Access to 2-Formyl Saturated Heterocycles and Unnatural Proline Derivatives. J Am Chem Soc 2023; 145:13715-13729. [PMID: 37327484 PMCID: PMC10330884 DOI: 10.1021/jacs.3c01985] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Alkene aminooxygenation and dioxygenation reactions that result in carbonyl products are uncommon, and protocols that control absolute stereochemistry are rare. We report herein catalytic enantioselective alkene aminooxygenation and dioxygenation that directly provide enantioenriched 2-formyl saturated heterocycles under aerobic conditions. Cyclization of substituted 4-pentenylsulfonamides, catalyzed by readily available chiral copper complexes and employing molecular oxygen as both oxygen source and stoichiometric oxidant, directly provides chiral 2-formyl pyrrolidines efficiently. Reductive or oxidative workup of these aldehydes provides their respective amino alcohols or amino acids (unnatural prolines). Enantioselective synthesis of an indoline and isoquinolines is also demonstrated. Concurrently, cyclization of various alkenols under similar conditions provides 2-formyl tetrahydrofurans, phthalans, isochromans, and morpholines. The nature of the copper ligands, the concentration of molecular oxygen, and the reaction temperature all impact the product distribution. Chiral nitrogen and oxygen heterocycles are common components of bioactive small molecules, and these enabling technologies provide access to saturated heterocycles functionalized with ready-to-use carbonyl electrophiles.
Collapse
Affiliation(s)
| | | | | | - Chaeeon Song
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Sherry R. Chemler
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, United States
| |
Collapse
|
2
|
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.
Collapse
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
| | | |
Collapse
|
3
|
Carbery A, Skyner R, von Delft F, Deane CM. Fragment Libraries Designed to Be Functionally Diverse Recover Protein Binding Information More Efficiently Than Standard Structurally Diverse Libraries. J Med Chem 2022; 65:11404-11413. [PMID: 35960886 PMCID: PMC9421645 DOI: 10.1021/acs.jmedchem.2c01004] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Current fragment-based drug design relies on the efficient exploration of chemical space by using structurally diverse libraries of small fragments. However, structurally dissimilar compounds can exploit the same interactions and thus be functionally similar. Using three-dimensional structures of many fragments bound to multiple targets, we examined if a better strategy for selecting fragments for screening libraries exists. We show that structurally diverse fragments can be described as functionally redundant, often making the same interactions. Ranking fragments by the number of novel interactions they made, we show that functionally diverse selections of fragments substantially increase the amount of information recovered for unseen targets compared to the amounts recovered by other methods of selection. Using these results, we design small functionally efficient libraries that can give significantly more information about new protein targets than similarly sized structurally diverse libraries. By covering more functional space, we can generate more diverse sets of drug leads.
Collapse
Affiliation(s)
- Anna Carbery
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, U.K.,Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
| | - Rachael Skyner
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
| | - Frank von Delft
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K.,Centre for Medicines Discovery, University of Oxford, Oxford OX3 7DQ, U.K
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, U.K
| |
Collapse
|
4
|
Boron-tethered oxidopyrylium-based [5 + 2] cycloadditions. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.154094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
5
|
Charoensutthivarakul S, Thomas SE, Curran A, Brown KP, Belardinelli JM, Whitehouse AJ, Acebrón-García-de-Eulate M, Sangan J, Gramani SG, Jackson M, Mendes V, Floto RA, Blundell TL, Coyne AG, Abell C. Development of Inhibitors of SAICAR Synthetase (PurC) from Mycobacterium abscessus Using a Fragment-Based Approach. ACS Infect Dis 2022; 8:296-309. [PMID: 35037462 PMCID: PMC7614835 DOI: 10.1021/acsinfecdis.1c00432] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mycobacterium abscessus (Mab) has emerged as a challenging threat to individuals with cystic fibrosis. Infections caused by this pathogen are often impossible to treat due to the intrinsic antibiotic resistance leading to lung malfunction and eventually death. Therefore, there is an urgent need to develop new drugs against novel targets in Mab to overcome drug resistance and subsequent treatment failure. In this study, SAICAR synthetase (PurC) from Mab was identified as a promising target for novel antibiotics. An in-house fragment library screen and a high-throughput X-ray crystallographic screen of diverse fragment libraries were explored to provide crucial starting points for fragment elaboration. A series of compounds developed from fragment growing and merging strategies, guided by crystallographic information and careful hit-to-lead optimization, have achieved potent nanomolar binding affinity against the enzyme. Some compounds also show a promising inhibitory effect against Mab and Mtb. This work utilizes a fragment-based design and demonstrates for the first time the potential to develop inhibitors against PurC from Mab.
Collapse
Affiliation(s)
- Sitthivut Charoensutthivarakul
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.,School of Bioinnovation and Bio-based Product Intelligence, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Sherine E Thomas
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Amy Curran
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Karen P Brown
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge CB23 3RE, United Kingdom
| | - Juan M Belardinelli
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Andrew J Whitehouse
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | | | - Jaspar Sangan
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge CB23 3RE, United Kingdom
| | - Subramanian G Gramani
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Vitor Mendes
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - R Andres Floto
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge CB23 3RE, United Kingdom
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Anthony G Coyne
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Chris Abell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| |
Collapse
|
6
|
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.
Collapse
|
7
|
Nichols C, Ng J, Keshu A, Kelly G, Conte MR, Marber MS, Fraternali F, De Nicola GF. Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1β-IL1R and p38α-TAB1 Complexes. J Med Chem 2020; 63:7559-7568. [PMID: 32543856 DOI: 10.1021/acs.jmedchem.0c00403] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nowadays, it is possible to combine X-ray crystallography and fragment screening in a medium throughput fashion to chemically probe the surfaces used by proteins to interact and use the outcome of the screens to systematically design protein-protein inhibitors. To prove it, we first performed a bioinformatics analysis of the Protein Data Bank protein complexes, which revealed over 400 cases where the crystal lattice of the target in the free form is such that large portions of the interacting surfaces are free from lattice contacts and therefore accessible to fragments during soaks. Among the tractable complexes identified, we then performed single fragment crystal screens on two particular interesting cases: the Il1β-ILR and p38α-TAB1 complexes. The result of the screens showed that fragments tend to bind in clusters, highlighting the small-molecule hotspots on the surface of the target protein. In most of the cases, the hotspots overlapped with the binding sites of the interacting proteins.
Collapse
Affiliation(s)
- Charlie Nichols
- British Heart Foundation Centre of Excellence, Department of Cardiology, The Rayne Institute, St Thomas' Hospital, King's College London, London SE1 7EH, U.K.,The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| | - Joseph Ng
- The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| | - Annika Keshu
- The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| | - Geoff Kelly
- NMR Facility, The Francis Crick Institute, London NW1 1AT, U.K
| | - Maria R Conte
- The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| | - Michael S Marber
- British Heart Foundation Centre of Excellence, Department of Cardiology, The Rayne Institute, St Thomas' Hospital, King's College London, London SE1 7EH, U.K
| | - Franca Fraternali
- The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| | - Gian F De Nicola
- British Heart Foundation Centre of Excellence, Department of Cardiology, The Rayne Institute, St Thomas' Hospital, King's College London, London SE1 7EH, U.K.,The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| |
Collapse
|
8
|
Bulandr JJ, Grabowski JP, Law CM, Shaw JL, Goodell JR, Mitchell TA. Investigation of Transfer Group, Tether Proximity, and Alkene Substitution for Intramolecular Silyloxypyrone-Based [5 + 2] Cycloadditions. J Org Chem 2019; 84:10306-10320. [PMID: 31322900 DOI: 10.1021/acs.joc.9b01479] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Systematic investigation of intramolecular silyloxypyrone-based [5 + 2] cycloadditions revealed three significant factors impacting conversion to cycloadduct: (1) the silyl transfer group has a substantial influence on the rate of reaction, and the robust t-butyldiphenylsilyl group was found to be more effective overall than the conventional t-butyldimethylsilyl group; (2) α,β-unsaturated esters were generally more reactive than terminal olefins and afforded appreciable quantity of cycloadduct even at room temperature; and (3) the proximity of the tether to the silyl transfer group revealed a critical alignment trend between the pyrone and the alkene. Taken together, these investigations provided insight regarding the steric and electronic parameters that impact the scope and limitation of these reactions.
Collapse
Affiliation(s)
- Jacob J Bulandr
- Department of Chemistry , Illinois State University , Campus Box 4160, Normal , Illinois 61790-4160 , United States
| | - Jacob P Grabowski
- Department of Chemistry , Illinois State University , Campus Box 4160, Normal , Illinois 61790-4160 , United States
| | - Chunyin M Law
- Department of Chemistry , Illinois State University , Campus Box 4160, Normal , Illinois 61790-4160 , United States
| | - Jessica L Shaw
- Department of Chemistry , Illinois State University , Campus Box 4160, Normal , Illinois 61790-4160 , United States
| | - John R Goodell
- Department of Chemistry , Illinois State University , Campus Box 4160, Normal , Illinois 61790-4160 , United States
| | - T Andrew Mitchell
- Department of Chemistry , Illinois State University , Campus Box 4160, Normal , Illinois 61790-4160 , United States
| |
Collapse
|
9
|
Thomas SE, Collins P, James RH, Mendes V, Charoensutthivarakul S, Radoux C, Abell C, Coyne AG, Floto RA, von Delft F, Blundell TL. Structure-guided fragment-based drug discovery at the synchrotron: screening binding sites and correlations with hotspot mapping. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2019; 377:20180422. [PMID: 31030650 PMCID: PMC6501894 DOI: 10.1098/rsta.2018.0422] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Structure-guided drug discovery emerged in the 1970s and 1980s, stimulated by the three-dimensional structures of protein targets that became available, mainly through X-ray crystal structure analysis, assisted by the development of synchrotron radiation sources. Structures of known drugs or inhibitors were used to guide the development of leads. The growth of high-throughput screening during the late 1980s and the early 1990s in the pharmaceutical industry of chemical libraries of hundreds of thousands of compounds of molecular weight of approximately 500 Da was impressive but still explored only a tiny fraction of the chemical space of the predicted 1040 drug-like compounds. The use of fragments with molecular weights less than 300 Da in drug discovery not only decreased the chemical space needing exploration but also increased promiscuity in binding targets. Here we discuss advances in X-ray fragment screening and the challenge of identifying sites where fragments not only bind but can be chemically elaborated while retaining their positions and binding modes. We first describe the analysis of fragment binding using conventional X-ray difference Fourier techniques, with Mycobacterium abscessus SAICAR synthetase (PurC) as an example. We observe that all fragments occupy positions predicted by computational hotspot mapping. We compare this with fragment screening at Diamond Synchrotron Light Source XChem facility using PanDDA software, which identifies many more fragment hits, only some of which bind to the predicted hotspots. Many low occupancy sites identified may not support elaboration to give adequate ligand affinity, although they will likely be useful in drug discovery as 'warm spots' for guiding elaboration of fragments bound at hotspots. We discuss implications of these observations for fragment screening at the synchrotron sources. This article is part of the theme issue 'Fifty years of synchrotron science: achievements and opportunities'.
Collapse
Affiliation(s)
- Sherine E. Thomas
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Patrick Collins
- Diamond Light Source (DLS), Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Rory Hennell James
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Vitor Mendes
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | | | - Chris Radoux
- The European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Anthony G. Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - R. Andres Floto
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge CB23 3RE, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC-Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Frank von Delft
- Diamond Light Source (DLS), Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
- e-mail:
| |
Collapse
|
10
|
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]
|
11
|
Khasiyatullina NR, Baronova TA, Mironova EV, Fayzullin RR, Litvinov IA, Efimov SV, Musin RZ, Klochkov VV, Mironov VF. Tandem dihetero-Diels–Alder and Huisgen cycloaddition reactions. Synthesis, crystal structure and hydrolysis of the novel cage phosphoranes. Org Chem Front 2018. [DOI: 10.1039/c8qo00915e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reaction of 2-(1-phenylvinyloxy)benzo-1,3,2-dioxaphosphole with activated carbonyl compounds leads to the stereoselective formation of cage phosphoranes.
Collapse
Affiliation(s)
- Nadezhda R. Khasiyatullina
- Arbuzov Institute of Organic and Physical Chemistry
- FRC Kazan Scientific Center of Russian Academy of Sciences
- 420088 Kazan
- Russian Federation
- Institute of Physics
| | - Tamara A. Baronova
- Arbuzov Institute of Organic and Physical Chemistry
- FRC Kazan Scientific Center of Russian Academy of Sciences
- 420088 Kazan
- Russian Federation
- Institute of Physics
| | - Ekaterina V. Mironova
- Arbuzov Institute of Organic and Physical Chemistry
- FRC Kazan Scientific Center of Russian Academy of Sciences
- 420088 Kazan
- Russian Federation
| | - Robert R. Fayzullin
- Arbuzov Institute of Organic and Physical Chemistry
- FRC Kazan Scientific Center of Russian Academy of Sciences
- 420088 Kazan
- Russian Federation
| | - Igor A. Litvinov
- Arbuzov Institute of Organic and Physical Chemistry
- FRC Kazan Scientific Center of Russian Academy of Sciences
- 420088 Kazan
- Russian Federation
| | - Sergey V. Efimov
- Institute of Physics
- Kazan Federal University
- 420008 Kazan
- Russian Federation
| | - Rashid Z. Musin
- Arbuzov Institute of Organic and Physical Chemistry
- FRC Kazan Scientific Center of Russian Academy of Sciences
- 420088 Kazan
- Russian Federation
| | | | - Vladimir F. Mironov
- Arbuzov Institute of Organic and Physical Chemistry
- FRC Kazan Scientific Center of Russian Academy of Sciences
- 420088 Kazan
- Russian Federation
- Institute of Physics
| |
Collapse
|