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Chevillard F, Kolb P. SCUBIDOO: A Large yet Screenable and Easily Searchable Database of Computationally Created Chemical Compounds Optimized toward High Likelihood of Synthetic Tractability. J Chem Inf Model 2015; 55:1824-35. [PMID: 26282054 DOI: 10.1021/acs.jcim.5b00203] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
De novo drug design is widely assisted by computational approaches that enable the generation of a tremendous amount of new virtual molecules within a short time frame. While the novelty of the computationally generated compounds can easily be assessed, such approaches often neglect the synthetic feasibility of the molecules, thus creating a potential hurdle that can be a barrier to further investigation. Therefore, we have developed SCUBIDOO, a freely accessible database concept that currently holds 21 million virtual products originating from a small library of building blocks and a collection of robust organic reactions. This large data set was reduced to three representative and computationally tractable samples denoted as S, M, and L, containing 9994, 99,977, and 999,794 products, respectively. These small sets are useful as starting points for ligand identification and optimization projects. The generated products come with synthesis instructions and alerts of possible side reactions, and we show that they exhibit drug-like properties while still extending into unexplored quadrants of chemical space, thus suggesting novelty. We show multiple examples that demonstrate how SCUBIDOO can facilitate the search around initial hits. This database might be a useful idea generator for early ligand discovery projects since it allows a focus on those molecules that are likely to be synthetically feasible and can therefore be studied further. Together with its modular building block construction principle, this database is also suitable for structure-activity relationship studies or fragment-growing strategies.
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Affiliation(s)
- F Chevillard
- Department of Pharmaceutical Chemistry, Philipps-University Marburg , 35032 Marburg, Germany
| | - P Kolb
- Department of Pharmaceutical Chemistry, Philipps-University Marburg , 35032 Marburg, Germany
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52
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Awale M, Reymond JL. Similarity Mapplet: Interactive Visualization of the Directory of Useful Decoys and ChEMBL in High Dimensional Chemical Spaces. J Chem Inf Model 2015. [PMID: 26207526 DOI: 10.1021/acs.jcim.5b00182] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
An Internet portal accessible at www.gdb.unibe.ch has been set up to automatically generate color-coded similarity maps of the ChEMBL database in relation to up to two sets of active compounds taken from the enhanced Directory of Useful Decoys (eDUD), a random set of molecules, or up to two sets of user-defined reference molecules. These maps visualize the relationships between the selected compounds and ChEMBL in six different high dimensional chemical spaces, namely MQN (42-D molecular quantum numbers), SMIfp (34-D SMILES fingerprint), APfp (20-D shape fingerprint), Xfp (55-D pharmacophore fingerprint), Sfp (1024-bit substructure fingerprint), and ECfp4 (1024-bit extended connectivity fingerprint). The maps are supplied in form of Java based desktop applications called "similarity mapplets" allowing interactive content browsing and linked to a "Multifingerprint Browser for ChEMBL" (also accessible directly at www.gdb.unibe.ch ) to perform nearest neighbor searches. One can obtain six similarity mapplets of ChEMBL relative to random reference compounds, 606 similarity mapplets relative to single eDUD active sets, 30,300 similarity mapplets relative to pairs of eDUD active sets, and any number of similarity mapplets relative to user-defined reference sets to help visualize the structural diversity of compound series in drug optimization projects and their relationship to other known bioactive compounds.
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Affiliation(s)
- Mahendra Awale
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
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Rastelli G, Pinzi L. Computational polypharmacology comes of age. Front Pharmacol 2015; 6:157. [PMID: 26283966 PMCID: PMC4516879 DOI: 10.3389/fphar.2015.00157] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 07/14/2015] [Indexed: 12/18/2022] Open
Affiliation(s)
- Giulio Rastelli
- Molecular Modelling and Drug Design Lab, Life Sciences Department, University of Modena and Reggio Emilia Modena, Italy
| | - Luca Pinzi
- Molecular Modelling and Drug Design Lab, Life Sciences Department, University of Modena and Reggio Emilia Modena, Italy
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54
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Rodrigues T, Reker D, Kunze J, Schneider P, Schneider G. Revealing the Macromolecular Targets of Fragment-Like Natural Products. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/anie.201504241] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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55
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Rodrigues T, Reker D, Kunze J, Schneider P, Schneider G. Revealing the Macromolecular Targets of Fragment-Like Natural Products. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504241] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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56
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Structure versus function—The impact of computational methods on the discovery of specific GPCR–ligands. Bioorg Med Chem 2015; 23:3907-12. [DOI: 10.1016/j.bmc.2015.03.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/06/2015] [Accepted: 03/09/2015] [Indexed: 12/26/2022]
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57
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Perna AM, Rodrigues T, Schmidt TP, Böhm M, Stutz K, Reker D, Pfeiffer B, Altmann KH, Backert S, Wessler S, Schneider G. Fragment-Based De Novo Design Reveals a Small-Molecule Inhibitor ofHelicobacter PyloriHtrA. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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58
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Perna AM, Rodrigues T, Schmidt TP, Böhm M, Stutz K, Reker D, Pfeiffer B, Altmann KH, Backert S, Wessler S, Schneider G. Fragment-Based De Novo Design Reveals a Small-Molecule Inhibitor of Helicobacter Pylori HtrA. Angew Chem Int Ed Engl 2015; 54:10244-8. [PMID: 26069090 DOI: 10.1002/anie.201504035] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Indexed: 01/22/2023]
Abstract
Sustained identification of innovative chemical entities is key for the success of chemical biology and drug discovery. We report the fragment-based, computer-assisted de novo design of a small molecule inhibiting Helicobacter pylori HtrA protease. Molecular binding of the designed compound to HtrA was confirmed through biophysical methods, supporting its functional activity in vitro. Hit expansion led to the identification of the currently best-in-class HtrA inhibitor. The results obtained reinforce the validity of ligand-based de novo design and binding-kinetics-guided optimization for the efficient discovery of pioneering lead structures and prototyping drug-like chemical probes with tailored bioactivity.
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Affiliation(s)
- Anna M Perna
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Tiago Rodrigues
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | | | - Manja Böhm
- Department of Biology, Universität Erlangen-Nürnberg (Germany)
| | - Katharina Stutz
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Daniel Reker
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Bernhard Pfeiffer
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Karl-Heinz Altmann
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Steffen Backert
- Department of Biology, Universität Erlangen-Nürnberg (Germany)
| | - Silja Wessler
- Department of Molecular Biology, Universität Salzburg (Austria)
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland).
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59
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Reker D, Schneider G. Active-learning strategies in computer-assisted drug discovery. Drug Discov Today 2015; 20:458-65. [DOI: 10.1016/j.drudis.2014.12.004] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 11/13/2014] [Accepted: 12/02/2014] [Indexed: 12/20/2022]
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60
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Gisbert Schneider. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201409126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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61
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Gisbert Schneider. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/anie.201409126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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62
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Rodrigues T, Lin YC, Hartenfeller M, Renner S, Lim YF, Schneider G. Repurposing de novo designed entities reveals phosphodiesterase 3B and cathepsin L modulators. Chem Commun (Camb) 2015; 51:7478-81. [DOI: 10.1039/c5cc01376c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Scaffold hopping: a computational algorithm correctly predicted the macromolecular target ofde novogenerated small molecular entities.
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Affiliation(s)
- Tiago Rodrigues
- Swiss Federal Institute of Technology (ETH)
- Department of Chemistry and Applied Biosciences
- 8093 Zürich
- Switzerland
| | - Yen-Chu Lin
- Swiss Federal Institute of Technology (ETH)
- Department of Chemistry and Applied Biosciences
- 8093 Zürich
- Switzerland
| | - Markus Hartenfeller
- Swiss Federal Institute of Technology (ETH)
- Department of Chemistry and Applied Biosciences
- 8093 Zürich
- Switzerland
- Novartis Pharma AG
| | | | - Yi Fan Lim
- Swiss Federal Institute of Technology (ETH)
- Department of Chemistry and Applied Biosciences
- 8093 Zürich
- Switzerland
| | - Gisbert Schneider
- Swiss Federal Institute of Technology (ETH)
- Department of Chemistry and Applied Biosciences
- 8093 Zürich
- Switzerland
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63
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Rodrigues T, Hauser N, Reker D, Reutlinger M, Wunderlin T, Hamon J, Koch G, Schneider G. Multidimensional de novo design reveals 5-HT2B receptor-selective ligands. Angew Chem Int Ed Engl 2014; 54:1551-5. [PMID: 25475886 DOI: 10.1002/anie.201410201] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 10/30/2014] [Indexed: 11/10/2022]
Abstract
We report a multi-objective de novo design study driven by synthetic tractability and aimed at the prioritization of computer-generated 5-HT2B receptor ligands with accurately predicted target-binding affinities. Relying on quantitative bioactivity models we designed and synthesized structurally novel, selective, nanomolar, and ligand-efficient 5-HT2B modulators with sustained cell-based effects. Our results suggest that seamless amalgamation of computational activity prediction and molecular design with microfluidics-assisted synthesis enables the swift generation of small molecules with the desired polypharmacology.
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Affiliation(s)
- Tiago Rodrigues
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich (Switzerland)
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64
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Rodrigues T, Hauser N, Reker D, Reutlinger M, Wunderlin T, Hamon J, Koch G, Schneider G. Multidimensional De Novo Design Reveals 5-HT2BReceptor-Selective Ligands. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410201] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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65
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Miyao T, Kaneko H, Funatsu K. Ring-System-Based Exhaustive Structure Generation for Inverse-QSPR/QSAR. Mol Inform 2014; 33:764-78. [PMID: 27485423 DOI: 10.1002/minf.201400072] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 09/23/2014] [Indexed: 11/06/2022]
Abstract
Inverse-QSPR/QSAR aims to solve the inverse problem of chemical structure generation based on QSPR/QSAR models, once the properties or activities are specified. To efficiently solve this problem, an exhaustive ring-system-based structure generation methodology was developed. The concept of the applicability domain (AD) is automatically acknowledged within the proposed strategy. The local AD is considered by introducing the probability distribution of a given data set, and the universal AD is considered using ring-system-based fragments in the training data set. Structures with desired properties or activities are enumerated by assembling fragments, including atomic elements, in a tree-like way. The usefulness of the proposed method is demonstrated through a case study of ligand design for the human alpha 2A adrenergic receptor (ADR2A_HUMAN). We succeeded in generating structures focusing only on a pre-defined region in chemical space, resulting in structures whose desired activity has a high likelihood being efficiently generated. In addition, the limitations of our proposed method and future challenges are discussed.
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Affiliation(s)
- Tomoyuki Miyao
- Department of Chemical System Engineering, Graduated of School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan phone: (+81) 3-5841-7751, fax: (+81) 3-5841-7771
| | - Hiromasa Kaneko
- Department of Chemical System Engineering, Graduated of School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan phone: (+81) 3-5841-7751, fax: (+81) 3-5841-7771
| | - Kimito Funatsu
- Department of Chemical System Engineering, Graduated of School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan phone: (+81) 3-5841-7751, fax: (+81) 3-5841-7771.
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