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Coley CW, Eyke NS, Jensen KF. Autonomous Discovery in the Chemical Sciences Part I: Progress. Angew Chem Int Ed Engl 2020; 59:22858-22893. [DOI: 10.1002/anie.201909987] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Connor W. Coley
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Natalie S. Eyke
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Klavs F. Jensen
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
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2
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Coley CW, Eyke NS, Jensen KF. Autonome Entdeckung in den chemischen Wissenschaften, Teil I: Fortschritt. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201909987] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Connor W. Coley
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Natalie S. Eyke
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Klavs F. Jensen
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
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3
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Friedrich L, Byrne R, Treder A, Singh I, Bauer C, Gudermann T, Mederos Y Schnitzler M, Storch U, Schneider G. Shape Similarity by Fractal Dimensionality: An Application in the de novo Design of (-)-Englerin A Mimetics. ChemMedChem 2020; 15:566-570. [PMID: 32162837 DOI: 10.1002/cmdc.202000017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/09/2020] [Indexed: 12/22/2022]
Abstract
Molecular shape and pharmacological function are interconnected. To capture shape, the fractal dimensionality concept was employed, providing a natural similarity measure for the virtual screening of de novo generated small molecules mimicking the structurally complex natural product (-)-englerin A. Two of the top-ranking designs were synthesized and tested for their ability to modulate transient receptor potential (TRP) cation channels which are cellular targets of (-)-englerin A. Intracellular calcium assays and electrophysiological whole-cell measurements of TRPC4 and TRPM8 channels revealed potent inhibitory effects of one of the computer-generated compounds. Four derivatives of this identified hit compound had comparable effects on TRPC4 and TRPM8. The results of this study corroborate the use of fractal dimensionality as an innovative shape-based molecular representation for molecular scaffold-hopping.
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Affiliation(s)
- Lukas Friedrich
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Ryan Byrne
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Aaron Treder
- Walther Straub Institute of Pharmacology and Toxicology, Ludwig Maximilians University of Munich, Goethestrasse 33, 80336, Munich, Germany
| | - Inderjeet Singh
- Walther Straub Institute of Pharmacology and Toxicology, Ludwig Maximilians University of Munich, Goethestrasse 33, 80336, Munich, Germany
| | - Christoph Bauer
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Thomas Gudermann
- Walther Straub Institute of Pharmacology and Toxicology, Ludwig Maximilians University of Munich, Goethestrasse 33, 80336, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, Biedersteiner Strasse 29, 80802, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), German Center for Lung Research, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Michael Mederos Y Schnitzler
- Walther Straub Institute of Pharmacology and Toxicology, Ludwig Maximilians University of Munich, Goethestrasse 33, 80336, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, Biedersteiner Strasse 29, 80802, Munich, Germany
| | - Ursula Storch
- Walther Straub Institute of Pharmacology and Toxicology, Ludwig Maximilians University of Munich, Goethestrasse 33, 80336, Munich, Germany.,Institute for Cardiovascular Prevention (IPEK), Ludwig Maximilians University of Munich, Pettenkoferstrasse 8a & 9, 80336, Munich, Germany
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
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Schneider G, Clark DE. Automated De Novo Drug Design: Are We Nearly There Yet? Angew Chem Int Ed Engl 2019; 58:10792-10803. [PMID: 30730601 DOI: 10.1002/anie.201814681] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Indexed: 11/09/2022]
Abstract
Medicinal chemistry and, in particular, drug design have often been perceived as more of an art than a science. The many unknowns of human disease and the sheer complexity of chemical space render decision making in medicinal chemistry exceptionally demanding. Computational models can assist the medicinal chemist in this endeavour. Provided here is an overview of recent examples of automated de novo molecular design, a discussion of the concepts and computational approaches involved, and the daring prediction of some of the possibilities and limitations of drug design using machine intelligence.
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Affiliation(s)
- Gisbert Schneider
- ETH Zurich, Department of Chemistry and Applied Biosciences, RETHINK, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - David E Clark
- Charles River, 6-9 Spire Green Centre, Harlow, Essex, CM19 5TR, UK
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5
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Schneider G, Clark DE. Automated De Novo Drug Design: Are We Nearly There Yet? Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814681] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Gisbert Schneider
- ETH ZurichDepartment of Chemistry and Applied Biosciences, RETHINK Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - David E. Clark
- Charles River 6–9 Spire Green Centre Harlow Essex CM19 5TR UK
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6
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Gold(I)-Catalysis for the Synthesis of Terpenoids: From Intramolecular Cascades to Intermolecular Cycloadditions. Isr J Chem 2018. [DOI: 10.1002/ijch.201800006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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7
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Kumarswamyreddy N, Kesavan V. Stereoselective and Regioselective Assembly of Spirooxindole [2,1-b]furan Motifs through a Tandem Friedel-Crafts Alkylation/5-exo-dig-Cyclization. European J Org Chem 2016. [DOI: 10.1002/ejoc.201601030] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Nandarapu Kumarswamyreddy
- Chemical Biology Laboratory; Department of Biotechnology; Indian Institute of Technology Madras; Bhupat and Jyoti Mehta School of Biosciences; Chennai 600036 India
| | - Venkitasamy Kesavan
- Chemical Biology Laboratory; Department of Biotechnology; Indian Institute of Technology Madras; Bhupat and Jyoti Mehta School of Biosciences; Chennai 600036 India
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8
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Schneider G, Reker D, Chen T, Hauenstein K, Schneider P, Altmann KH. Deorphaning the Macromolecular Targets of the Natural Anticancer Compound Doliculide. Angew Chem Int Ed Engl 2016; 55:12408-11. [PMID: 27605391 DOI: 10.1002/anie.201605707] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/11/2016] [Indexed: 11/06/2022]
Abstract
The cyclodepsipeptide doliculide is a marine natural product with strong actin-polymerizing and anticancer activities. Evidence for doliculide acting as a potent and subtype-selective antagonist of prostanoid E receptor 3 (EP3) is presented. Computational target prediction suggested that this membrane receptor is a likely macromolecular target and enabled immediate in vitro validation. This proof-of-concept study demonstrates the in silico deorphanization of phenotypic screening hits as a viable concept for future natural-product-inspired chemical biology and drug discovery efforts.
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Affiliation(s)
- Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zürich, Switzerland.
| | - Daniel Reker
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zürich, Switzerland
| | - Tao Chen
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zürich, Switzerland
| | - Kurt Hauenstein
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zürich, Switzerland
| | - Petra Schneider
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zürich, Switzerland.,inSili.com LLC, Zürich, Switzerland
| | - Karl-Heinz Altmann
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zürich, Switzerland
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9
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Schneider G, Reker D, Chen T, Hauenstein K, Schneider P, Altmann KH. Deorphaning the Macromolecular Targets of the Natural Anticancer Compound Doliculide. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605707] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Gisbert Schneider
- Department of Chemistry and Applied Biosciences; Institute of Pharmaceutical Sciences; ETH Zürich; Wolfgang-Pauli-Strasse 10 8093 Zürich Switzerland
| | - Daniel Reker
- Department of Chemistry and Applied Biosciences; Institute of Pharmaceutical Sciences; ETH Zürich; Wolfgang-Pauli-Strasse 10 8093 Zürich Switzerland
| | - Tao Chen
- Department of Chemistry and Applied Biosciences; Institute of Pharmaceutical Sciences; ETH Zürich; Wolfgang-Pauli-Strasse 10 8093 Zürich Switzerland
| | - Kurt Hauenstein
- Department of Chemistry and Applied Biosciences; Institute of Pharmaceutical Sciences; ETH Zürich; Wolfgang-Pauli-Strasse 10 8093 Zürich Switzerland
| | - Petra Schneider
- Department of Chemistry and Applied Biosciences; Institute of Pharmaceutical Sciences; ETH Zürich; Wolfgang-Pauli-Strasse 10 8093 Zürich Switzerland
- inSili.com LLC; Zürich Switzerland
| | - Karl-Heinz Altmann
- Department of Chemistry and Applied Biosciences; Institute of Pharmaceutical Sciences; ETH Zürich; Wolfgang-Pauli-Strasse 10 8093 Zürich Switzerland
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10
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Rodrigues T, Sieglitz F, Somovilla VJ, Cal PMSD, Galione A, Corzana F, Bernardes GJL. Unveiling (-)-Englerin A as a Modulator of L-Type Calcium Channels. Angew Chem Int Ed Engl 2016; 55:11077-81. [PMID: 27391219 PMCID: PMC5042069 DOI: 10.1002/anie.201604336] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Indexed: 11/11/2022]
Abstract
The voltage-dependent L-type Ca(2+) channel was identified as a macromolecular target for (-)-englerin A. This finding was reached by using an unprecedented ligand-based prediction platform and the natural product piperlongumine as a pharmacophore probe. (-)-Englerin A features high substructure dissimilarity to known ligands for voltage-dependent Ca(2+) channels, selective binding affinity for the dihydropyridine site, and potent modulation of calcium signaling in muscle cells and vascular tissue. The observed activity was rationalized at the atomic level by molecular dynamics simulations. Experimental confirmation of this hitherto unknown macromolecular target expands the bioactivity space for this natural product and corroborates the effectiveness of chemocentric computational methods for prioritizing target-based screens and identifying binding counterparts of complex natural products.
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Affiliation(s)
- Tiago Rodrigues
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal.
| | - Florian Sieglitz
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Víctor J Somovilla
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de la Rioja, 26006, Logroño, Spain
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Pedro M S D Cal
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Antony Galione
- Department of Pharmacology, University of Oxford, Mansfield Road, OX1 3QT, Oxford, UK
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de la Rioja, 26006, Logroño, Spain.
| | - Gonçalo J L Bernardes
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal. ,
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK. ,
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11
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Rodrigues T, Sieglitz F, Somovilla VJ, Cal PMSD, Galione A, Corzana F, Bernardes GJL. Unveiling (−)-Englerin A as a Modulator of L-Type Calcium Channels. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604336] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tiago Rodrigues
- Instituto de Medicina Molecular; Faculdade de Medicina da Universidade de Lisboa; Av. Prof. Egas Moniz 1649-028 Lisboa Portugal
| | - Florian Sieglitz
- Instituto de Medicina Molecular; Faculdade de Medicina da Universidade de Lisboa; Av. Prof. Egas Moniz 1649-028 Lisboa Portugal
| | - Víctor J. Somovilla
- Departamento de Química, Centro de Investigación en Síntesis Química; Universidad de la Rioja; 26006 Logroño Spain
- Department of Chemistry; University of Cambridge; Lensfield Road CB2 1EW Cambridge UK
| | - Pedro M. S. D. Cal
- Instituto de Medicina Molecular; Faculdade de Medicina da Universidade de Lisboa; Av. Prof. Egas Moniz 1649-028 Lisboa Portugal
| | - Antony Galione
- Department of Pharmacology; University of Oxford; Mansfield Road OX1 3QT Oxford UK
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis Química; Universidad de la Rioja; 26006 Logroño Spain
| | - Gonçalo J. L. Bernardes
- Instituto de Medicina Molecular; Faculdade de Medicina da Universidade de Lisboa; Av. Prof. Egas Moniz 1649-028 Lisboa Portugal
- Department of Chemistry; University of Cambridge; Lensfield Road CB2 1EW Cambridge UK
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