1
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Pujol‐Giménez J, Poirier M, Bühlmann S, Schuppisser C, Bhardwaj R, Awale M, Visini R, Javor S, Hediger MA, Reymond J. Inhibitors of Human Divalent Metal Transporters DMT1 (SLC11A2) and ZIP8 (SLC39A8) from a GDB-17 Fragment Library. ChemMedChem 2021; 16:3306-3314. [PMID: 34309203 PMCID: PMC8596699 DOI: 10.1002/cmdc.202100467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 11/06/2022]
Abstract
Solute carrier proteins (SLCs) are membrane proteins controlling fluxes across biological membranes and represent an emerging class of drug targets. Here we searched for inhibitors of divalent metal transporters in a library of 1,676 commercially available 3D-shaped fragment-like molecules from the generated database GDB-17, which lists all possible organic molecules up to 17 atoms of C, N, O, S and halogen following simple criteria for chemical stability and synthetic feasibility. While screening against DMT1 (SLC11A2), an iron transporter associated with hemochromatosis and for which only very few inhibitors are known, only yielded two weak inhibitors, our approach led to the discovery of the first inhibitor of ZIP8 (SLC39A8), a zinc transporter associated with manganese homeostasis and osteoarthritis but with no previously reported pharmacology, demonstrating that this target is druggable.
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Affiliation(s)
- Jonai Pujol‐Giménez
- Department of Biomedical Research and Department of Nephrology and Hypertension Membrane Transport Discovery Lab Inselspital, Bern University HospitalUniversity of BernCH-3010BernSwitzerland
| | - Marion Poirier
- Department of Chemistry Biochemistry and Pharmaceutical SciencesUniversity of BernFreiestrasse 33012BernSwitzerland
| | - Sven Bühlmann
- Department of Chemistry Biochemistry and Pharmaceutical SciencesUniversity of BernFreiestrasse 33012BernSwitzerland
| | - Céline Schuppisser
- Department of Chemistry Biochemistry and Pharmaceutical SciencesUniversity of BernFreiestrasse 33012BernSwitzerland
| | - Rajesh Bhardwaj
- Department of Biomedical Research and Department of Nephrology and Hypertension Membrane Transport Discovery Lab Inselspital, Bern University HospitalUniversity of BernCH-3010BernSwitzerland
| | - Mahendra Awale
- Department of Chemistry Biochemistry and Pharmaceutical SciencesUniversity of BernFreiestrasse 33012BernSwitzerland
| | - Ricardo Visini
- Department of Chemistry Biochemistry and Pharmaceutical SciencesUniversity of BernFreiestrasse 33012BernSwitzerland
| | - Sacha Javor
- Department of Chemistry Biochemistry and Pharmaceutical SciencesUniversity of BernFreiestrasse 33012BernSwitzerland
| | - Matthias A. Hediger
- Department of Biomedical Research and Department of Nephrology and Hypertension Membrane Transport Discovery Lab Inselspital, Bern University HospitalUniversity of BernCH-3010BernSwitzerland
| | - Jean‐Louis Reymond
- Department of Chemistry Biochemistry and Pharmaceutical SciencesUniversity of BernFreiestrasse 33012BernSwitzerland
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2
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Meier K, Arús‐Pous J, Reymond J. A Potent and Selective Janus Kinase Inhibitor with a Chiral 3D‐Shaped Triquinazine Ring System from Chemical Space. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kris Meier
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Josep Arús‐Pous
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Jean‐Louis Reymond
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 3012 Bern Switzerland
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3
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Morgado A, Najera F, Lagunas A, Samitier J, Vida Y, Perez-Inestrosa E. Slightly congested amino terminal dendrimers. The synthesis of amide-based stable structures on a large scale. Polym Chem 2021. [DOI: 10.1039/d1py00667c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Preparation of a new family of stable and aqueous soluble high-generation aliphatic polyamide amino terminal dendrimers. Promising scaffolds for applications where the combination of stability, multivalence and efficient conjugation is required.
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Affiliation(s)
- Anjara Morgado
- Universidad de Málaga - IBIMA, Dpto. Química Orgánica, Campus de Teatinos s/n, 29071 Málaga, Spain
- Centro Andaluz de Nanomedicina y Biotecnología-BIONAND. Parque Tecnológico de Andalucía, c/Severo Ochoa, 35, 29590 Campanillas, Málaga, Spain
| | - Francisco Najera
- Universidad de Málaga - IBIMA, Dpto. Química Orgánica, Campus de Teatinos s/n, 29071 Málaga, Spain
- Centro Andaluz de Nanomedicina y Biotecnología-BIONAND. Parque Tecnológico de Andalucía, c/Severo Ochoa, 35, 29590 Campanillas, Málaga, Spain
| | - Anna Lagunas
- Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
| | - Josep Samitier
- Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
- Department of Electronics and Biomedical Engineering, University of Barcelona (UB), 08028 Barcelona, Spain
| | - Yolanda Vida
- Universidad de Málaga - IBIMA, Dpto. Química Orgánica, Campus de Teatinos s/n, 29071 Málaga, Spain
- Centro Andaluz de Nanomedicina y Biotecnología-BIONAND. Parque Tecnológico de Andalucía, c/Severo Ochoa, 35, 29590 Campanillas, Málaga, Spain
| | - Ezequiel Perez-Inestrosa
- Universidad de Málaga - IBIMA, Dpto. Química Orgánica, Campus de Teatinos s/n, 29071 Málaga, Spain
- Centro Andaluz de Nanomedicina y Biotecnología-BIONAND. Parque Tecnológico de Andalucía, c/Severo Ochoa, 35, 29590 Campanillas, Málaga, Spain
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4
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Meier K, Arús‐Pous J, Reymond J. A Potent and Selective Janus Kinase Inhibitor with a Chiral 3D‐Shaped Triquinazine Ring System from Chemical Space. Angew Chem Int Ed Engl 2020; 60:2074-2077. [DOI: 10.1002/anie.202012049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/25/2020] [Indexed: 01/31/2023]
Affiliation(s)
- Kris Meier
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Josep Arús‐Pous
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Jean‐Louis Reymond
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 3012 Bern Switzerland
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5
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Abstract
Advances in computer processing speed and storage capacity have enabled researchers to generate virtual chemical libraries containing billions of molecules. While these numbers appear large, they are only a small fraction of the number of organic molecules that could potentially be synthesized. This review provides an overview of recent advances in the generation and use of virtual chemical libraries in medicinal chemistry. We also consider the practical implications of these libraries in drug discovery programs and highlight a number of current and future challenges.
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Affiliation(s)
- W Patrick Walters
- Relay Therapeutics , 215 First Street , Cambridge , Massachusetts 02142 , United States
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6
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Visini R, Arús-Pous J, Awale M, Reymond JL. Virtual Exploration of the Ring Systems Chemical Universe. J Chem Inf Model 2017; 57:2707-2718. [PMID: 29019686 DOI: 10.1021/acs.jcim.7b00457] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Here, we explore the chemical space of all virtually possible organic molecules focusing on ring systems, which represent the cyclic cores of organic molecules obtained by removing all acyclic bonds and converting all remaining atoms to carbon. This approach circumvents the combinatorial explosion encountered when enumerating the molecules themselves. We report the chemical universe database GDB4c containing 916 130 ring systems up to four saturated or aromatic rings and maximum ring size of 14 atoms and GDB4c3D containing the corresponding 6 555 929 stereoisomers. Almost all (98.6%) of these ring systems are unknown and represent chiral 3D-shaped macrocycles containing small rings and quaternary centers reminiscent of polycyclic natural products. We envision that GDB4c can serve to select new ring systems from which to design analogs of such natural products. The database is available for download at www.gdb.unibe.ch together with interactive visualization and search tools as a resource for molecular design.
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Affiliation(s)
- Ricardo Visini
- Department of Chemistry and Biochemistry, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Josep Arús-Pous
- Department of Chemistry and Biochemistry, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Mahendra Awale
- Department of Chemistry and Biochemistry, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
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7
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Abstract
To better understand chemical space we recently enumerated the database GDB-17 containing 166.4 billion possible molecules up to 17 atoms of C, N, O, S and halogen following the simple rules of chemical stability and synthetic feasibility. However, due to the combinatorial explosion caused by systematic enumeration GDB-17 is strongly biased toward the largest, functionally and stereochemically most complex molecules and far too large for most virtual screening tools. Herein we selected a much smaller subset of GDB-17, called the fragment database FDB-17, which contains 10 million fragmentlike molecules evenly covering a broad value range for molecular size, polarity, and stereochemical complexity. The database is available at www.gdb.unibe.ch for download and free use, together with an interactive visualization application and a Web-based nearest neighbor search tool to facilitate the selection of new fragment-sized molecules for chemical synthesis.
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Affiliation(s)
- Ricardo Visini
- Department of Chemistry and Biochemistry, University of Bern , Freiestrasse 3, 3012 Berne, Switzerland
| | - Mahendra Awale
- Department of Chemistry and Biochemistry, University of Bern , Freiestrasse 3, 3012 Berne, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Bern , Freiestrasse 3, 3012 Berne, Switzerland
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9
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Gaudêncio SP, Pereira F. Dereplication: racing to speed up the natural products discovery process. Nat Prod Rep 2015; 32:779-810. [PMID: 25850681 DOI: 10.1039/c4np00134f] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering: 1993-2014 (July)To alleviate the dereplication holdup, which is a major bottleneck in natural products discovery, scientists have been conducting their research efforts to add tools to their "bag of tricks" aiming to achieve faster, more accurate and efficient ways to accelerate the pace of the drug discovery process. Consequently dereplication has become a hot topic presenting a huge publication boom since 2012, blending multidisciplinary fields in new ways that provide important conceptual and/or methodological advances, opening up pioneering research prospects in this field.
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Affiliation(s)
- Susana P Gaudêncio
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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10
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Abstract
One of the simplest questions that can be asked about molecular diversity is how many organic molecules are possible in total? To answer this question, my research group has computationally enumerated all possible organic molecules up to a certain size to gain an unbiased insight into the entire chemical space. Our latest database, GDB-17, contains 166.4 billion molecules of up to 17 atoms of C, N, O, S, and halogens, by far the largest small molecule database reported to date. Molecules allowed by valency rules but unstable or nonsynthesizable due to strained topologies or reactive functional groups were not considered, which reduced the enumeration by at least 10 orders of magnitude and was essential to arrive at a manageable database size. Despite these restrictions, GDB-17 is highly relevant with respect to known molecules. Beyond enumeration, understanding and exploiting GDBs (generated databases) led us to develop methods for virtual screening and visualization of very large databases in the form of a "periodic system of molecules" comprising six different fingerprint spaces, with web-browsers for nearest neighbor searches, and the MQN- and SMIfp-Mapplet application for exploring color-coded principal component maps of GDB and other large databases. Proof-of-concept applications of GDB for drug discovery were realized by combining virtual screening with chemical synthesis and activity testing for neurotransmitter receptor and transporter ligands. One surprising lesson from using GDB for drug analog searches is the incredible depth of chemical space, that is, the fact that millions of very close analogs of any molecule can be readily identified by nearest-neighbor searches in the MQN-space of the various GDBs. The chemical space project has opened an unprecedented door on chemical diversity. Ongoing and yet unmet challenges concern enumerating molecules beyond 17 atoms and synthesizing GDB molecules with innovative scaffolds and pharmacophores.
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Affiliation(s)
- Jean-Louis Reymond
- Department of Chemistry and
Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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11
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Asymmetric synthesis of all four stereoisomers of 1-amino-3-hydroxy-cyclopentane-1-carboxylic acid. Tetrahedron 2015. [DOI: 10.1016/j.tet.2014.12.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Awale M, Reymond JL. Atom Pair 2D-Fingerprints Perceive 3D-Molecular Shape and Pharmacophores for Very Fast Virtual Screening of ZINC and GDB-17. J Chem Inf Model 2014; 54:1892-907. [DOI: 10.1021/ci500232g] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mahendra Awale
- Department of Chemistry and
Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and
Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne Switzerland
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13
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Peng Z. Very large virtual compound spaces: construction, storage and utility in drug discovery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2013; 10:e387-e394. [PMID: 24050135 DOI: 10.1016/j.ddtec.2013.01.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Recent activities in the construction, storage and exploration of very large virtual compound spaces are reviewed by this report. As expected, the systematic exploration of compound spaces at the highest resolution (individual atoms and bonds) is intrinsically intractable. By contrast, by staying within a finite number of reactions and a finite number of reactants or fragments, several virtual compound spaces have been constructed in a combinatorial fashion with sizes ranging from 10(11)11 to 10(20)20 compounds. Multiple search methods have been developed to perform searches (e.g. similarity, exact and substructure) into those compound spaces without the need for full enumeration. The up-front investment spent on synthetic feasibility during the construction of some of those virtual compound spaces enables a wider adoption by medicinal chemists to design and synthesize important compounds for drug discovery. Recent activities in the area of exploring virtual compound spaces via the evolutionary approach based on Genetic Algorithm also suggests a positive shift of focus from method development to workflow, integration and ease of use, all of which are required for this approach to be widely adopted by medicinal chemists.
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14
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Virshup AM, Contreras-García J, Wipf P, Yang W, Beratan DN. Stochastic voyages into uncharted chemical space produce a representative library of all possible drug-like compounds. J Am Chem Soc 2013; 135:7296-303. [PMID: 23548177 PMCID: PMC3670418 DOI: 10.1021/ja401184g] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The "small molecule universe" (SMU), the set of all synthetically feasible organic molecules of 500 Da molecular weight or less, is estimated to contain over 10(60) structures, making exhaustive searches for structures of interest impractical. Here, we describe the construction of a "representative universal library" spanning the SMU that samples the full extent of feasible small molecule chemistries. This library was generated using the newly developed Algorithm for Chemical Space Exploration with Stochastic Search (ACSESS). ACSESS makes two important contributions to chemical space exploration: it allows the systematic search of the unexplored regions of the small molecule universe, and it facilitates the mining of chemical libraries that do not yet exist, providing a near-infinite source of diverse novel compounds.
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Affiliation(s)
- Aaron M. Virshup
- Center for Chemical Methodologies and Library Development, Department of Chemistry, Duke University, Durham, NC 27708
| | - Julia Contreras-García
- Center for Chemical Methodologies and Library Development, Department of Chemistry, Duke University, Durham, NC 27708
| | - Peter Wipf
- Center for Chemical Methodologies and Library Development, Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260
| | - Weitao Yang
- Center for Chemical Methodologies and Library Development, Department of Chemistry, Duke University, Durham, NC 27708
| | - David N. Beratan
- Center for Chemical Methodologies and Library Development, Department of Chemistry, Duke University, Durham, NC 27708
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15
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Ruddigkeit L, Blum LC, Reymond JL. Visualization and virtual screening of the chemical universe database GDB-17. J Chem Inf Model 2013; 53:56-65. [PMID: 23259841 DOI: 10.1021/ci300535x] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The chemical universe database GDB-17 contains 166.4 billion molecules of up to 17 atoms of C, N, O, S, and halogens obeying rules for chemical stability, synthetic feasibility, and medicinal chemistry. GDB-17 was analyzed using 42 integer value descriptors of molecular structure which we term "Molecular Quantum Numbers" (MQN). Principal component analysis and representation of the (PC1, PC2)-plane provided a graphical overview of the GDB-17 chemical space. Rapid ligand-based virtual screening (LBVS) of GDB-17 using the city-block distance CBD(MQN) as a similarity search measure was enabled by a hashed MQN-fingerprint. LBVS of the entire GDB-17 and of selected subsets identified shape similar, scaffold hopping analogs (ROCS > 1.6 and T(SF) < 0.5) of 15 drugs. Over 97% of these analogs occurred within CBD(MQN) ≤ 12 from each drug, a constraint which might help focus advanced virtual screening. An MQN-searchable 50 million subset of GDB-17 is publicly available at www.gdb.unibe.ch .
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Affiliation(s)
- Lars Ruddigkeit
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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16
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Ruddigkeit L, van Deursen R, Blum LC, Reymond JL. Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17. J Chem Inf Model 2012; 52:2864-75. [DOI: 10.1021/ci300415d] [Citation(s) in RCA: 629] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Lars Ruddigkeit
- Department
of Chemistry and Biochemistry, NCCR TransCure, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Ruud van Deursen
- Biomolecular Screening Facility,
NCCR Chemical Biology, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015
Lausanne, Switzerland
| | - Lorenz C. Blum
- Department
of Chemistry and Biochemistry, NCCR TransCure, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Jean-Louis Reymond
- Department
of Chemistry and Biochemistry, NCCR TransCure, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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17
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Reymond JL, Awale M. Exploring chemical space for drug discovery using the chemical universe database. ACS Chem Neurosci 2012; 3:649-57. [PMID: 23019491 DOI: 10.1021/cn3000422] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 04/25/2012] [Indexed: 01/20/2023] Open
Abstract
Herein we review our recent efforts in searching for bioactive ligands by enumeration and virtual screening of the unknown chemical space of small molecules. Enumeration from first principles shows that almost all small molecules (>99.9%) have never been synthesized and are still available to be prepared and tested. We discuss open access sources of molecules, the classification and representation of chemical space using molecular quantum numbers (MQN), its exhaustive enumeration in form of the chemical universe generated databases (GDB), and examples of using these databases for prospective drug discovery. MQN-searchable GDB, PubChem, and DrugBank are freely accessible at www.gdb.unibe.ch.
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Affiliation(s)
- Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Mahendra Awale
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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18
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Takaishi M, Kudo F, Eguchi T. A Unique Pathway for the 3-Aminobutyrate Starter Unit from l-Glutamate through β-Glutamate during Biosynthesis of the 24-Membered Macrolactam Antibiotic, Incednine. Org Lett 2012; 14:4591-3. [DOI: 10.1021/ol302052c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Makoto Takaishi
- Department of Chemistry and Materials Science and Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Fumitaka Kudo
- Department of Chemistry and Materials Science and Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry and Materials Science and Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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19
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Bréthous L, Garcia-Delgado N, Schwartz J, Bertrand S, Bertrand D, Reymond JL. Synthesis and Nicotinic Receptor Activity of Chemical Space Analogues of N-(3R)-1-Azabicyclo[2.2.2]oct-3-yl-4-chlorobenzamide (PNU-282,987) and 1,4-Diazabicyclo[3.2.2]nonane-4-carboxylic Acid 4-Bromophenyl Ester (SSR180711). J Med Chem 2012; 55:4605-18. [DOI: 10.1021/jm300030r] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lise Bréthous
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Noemi Garcia-Delgado
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Julian Schwartz
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Sonia Bertrand
- HiQScreen, 15 rue de l'Athénée, 1206 Geneva, Switzerland
| | | | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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20
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Reymond JL, Ruddigkeit L, Blum L, van Deursen R. The enumeration of chemical space. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1104] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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21
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Reymond JL, van Deursen R, Bertrand D. What we have learned from crystal structures of proteins to receptor function. Biochem Pharmacol 2011; 82:1521-7. [DOI: 10.1016/j.bcp.2011.07.061] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/04/2011] [Accepted: 07/06/2011] [Indexed: 12/13/2022]
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22
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Blum LC, van Deursen R, Bertrand S, Mayer M, Bürgi JJ, Bertrand D, Reymond JL. Discovery of α7-Nicotinic Receptor Ligands by Virtual Screening of the Chemical Universe Database GDB-13. J Chem Inf Model 2011; 51:3105-12. [DOI: 10.1021/ci200410u] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Lorenz C. Blum
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Ruud van Deursen
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Sonia Bertrand
- HiQScreen, 15 rue de l’Athénée, 1206 Geneva, Switzerland
| | - Milena Mayer
- HiQScreen, 15 rue de l’Athénée, 1206 Geneva, Switzerland
| | - Justus J. Bürgi
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | | | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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23
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Blum LC, van Deursen R, Reymond JL. Visualisation and subsets of the chemical universe database GDB-13 for virtual screening. J Comput Aided Mol Des 2011; 25:637-47. [DOI: 10.1007/s10822-011-9436-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 05/13/2011] [Indexed: 10/18/2022]
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24
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Boehm M. Virtual Screening of Chemical Space: From Generic Compound Collections to Tailored Screening Libraries. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/9783527633326.ch1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
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25
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Nonell-Canals A, Mestres J. In Silico Target Profiling of One Billion Molecules. Mol Inform 2011; 30:405-9. [DOI: 10.1002/minf.201100018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 03/16/2011] [Indexed: 02/04/2023]
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Venhorst J, Núñez S, Kruse CG. Design of a high fragment efficiency library by molecular graph theory. ACS Med Chem Lett 2010; 1:499-503. [PMID: 24900238 DOI: 10.1021/ml100163s] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Accepted: 09/01/2010] [Indexed: 11/28/2022] Open
Abstract
Molecular graph theory was used to design a unique and diverse, high-efficiency fragment screening collection. A data set retrieved from the annotated database AurSCOPE GPS was used as the reference set, and the GDB-13 database, a virtual library of enumerated organic molecules, was used as a source for the fragment selection. The data graph collection of Discngine as implemented in PipelinePilot was applied to perform the graph pharmacophore similarity matching between the reference and the GDB-13 data sets, leading to the ultimate fragment screening library. The relevance of this unique fragment collection was demonstrated by means of a virtual screening exercise using human trypsin as a test case. Several novel entities with high similarity to known trypsin inhibitors were identified in the in silico exercise. The application of this unique, high fragment efficiency collection to other protein targets in the framework of fragment-based drug discovery is warranted.
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Affiliation(s)
| | - Sara Núñez
- Abbott Healthcare Products, 1381 CP Weesp, The Netherlands
| | - Chris G. Kruse
- Abbott Healthcare Products, 1381 CP Weesp, The Netherlands
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Garcia-Delgado N, Bertrand S, Nguyen KT, van Deursen R, Bertrand D, Reymond JL. Exploring α7-Nicotinic Receptor Ligand Diversity by Scaffold Enumeration from the Chemical Universe Database GDB. ACS Med Chem Lett 2010; 1:422-6. [PMID: 24900227 DOI: 10.1021/ml100125f] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 07/13/2010] [Indexed: 02/08/2023] Open
Abstract
Virtual analogues (1167860 compounds) of the nicotinic α7-receptor (α7 nAChR) ligands PNU-282,987 and SSR180711 were generated from the chemical universe database GDB-11 by extracting all aliphatic diamine analogues of the aminoquinuclidine and 1,4-diazabicyclo[3.2.2]nonane scaffolds of these ligands and converting them to the corresponding aryl amides using five different aromatic acyl groups. The library was ranked by docking to the nicotinic binding site of the acetylcholine binding protein (AChBP, 1UW6.pdb) using Autodock and Glide. Thirty-eight ligands derived from the best docking hits were synthesized and tested for modulation of the acetylcholine signal at the human α7 nAChR receptor expressed in Xenopus oocytes, leading to competitive and noncompetitive antagonists with IC50 = 5-7 μM. These experiments demonstrate the first example of using GDB in a fragment-based approach by diversifying the scaffold of known drugs.
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Affiliation(s)
- Noemi Garcia-Delgado
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Sonia Bertrand
- Department of Neuroscience, Medical Faculty, 1, rue Michel Servet CH-1211 Geneva 4, Switzerland
| | - Kong T. Nguyen
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Ruud van Deursen
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Daniel Bertrand
- Department of Neuroscience, Medical Faculty, 1, rue Michel Servet CH-1211 Geneva 4, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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Luethi E, Nguyen KT, Bürzle M, Blum LC, Suzuki Y, Hediger M, Reymond JL. Identification of selective norbornane-type aspartate analogue inhibitors of the glutamate transporter 1 (GLT-1) from the chemical universe generated database (GDB). J Med Chem 2010; 53:7236-50. [PMID: 20812729 DOI: 10.1021/jm100959g] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A variety of conformationally constrained aspartate and glutamate analogues inhibit the glutamate transporter 1 (GLT-1, also known as EAAT2). To expand the search for such analogues, a virtual library of aliphatic aspartate and glutamate analogues was generated starting from the chemical universe database GDB-11, which contains 26.4 million possible molecules up to 11 atoms of C, N, O, F, resulting in 101026 aspartate analogues and 151285 glutamate analogues. Virtual screening was realized by high-throughput docking to the glutamate binding site of the glutamate transporter homologue from Pyrococcus horikoshii (PDB code: 1XFH ) using Autodock. Norbornane-type aspartate analogues were selected from the top-scoring virtual hits and synthesized. Testing and optimization led to the identification of (1R*,2R*,3S*,4R*,6R*)-2-amino-6-phenethyl-bicyclo[2.2.1]heptane-2,3-dicarboxylic acid as a new inhibitor of GLT-1 with IC(50) = 1.4 μM against GLT-1 and no inhibition of the related transporter EAAC1. The systematic diversification of known ligands by enumeration with help of GDB followed by virtual screening, synthesis, and testing as exemplified here provides a general strategy for drug discovery.
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Affiliation(s)
- Erika Luethi
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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Affiliation(s)
- Ruud van Deursen
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012 Berne, Switzerland
| | - Lorenz C. Blum
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012 Berne, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012 Berne, Switzerland
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Reymond JL, van Deursen R, Blum LC, Ruddigkeit L. Chemical space as a source for new drugs. MEDCHEMCOMM 2010. [DOI: 10.1039/c0md00020e] [Citation(s) in RCA: 210] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Nguyen KT, Luethi E, Syed S, Urwyler S, Bertrand S, Bertrand D, Reymond JL. 3-(Aminomethyl)piperazine-2,5-dione as a novel NMDA glycine site inhibitor from the chemical universe database GDB. Bioorg Med Chem Lett 2009; 19:3832-5. [DOI: 10.1016/j.bmcl.2009.04.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Revised: 04/01/2009] [Accepted: 04/03/2009] [Indexed: 12/01/2022]
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Blum LC, Reymond JL. 970 Million Druglike Small Molecules for Virtual Screening in the Chemical Universe Database GDB-13. J Am Chem Soc 2009; 131:8732-3. [DOI: 10.1021/ja902302h] [Citation(s) in RCA: 423] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lorenz C. Blum
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012 Berne, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012 Berne, Switzerland
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