Chemical space; Virtual screening; acetyl choline receptors; computer-aided drug design; databases; cheminformatics
Reymond Jean-Louis, Visini Ricardo, Awale Mahendra, Erlanson Ed. D.A., Jahnke W. (2016), Fragment-based Drug Discovery, in Carmot Therapeutics (ed.), Wiley-VCH, Weinheim, 57-75.
Jin Xian, Awale Mahendra, Zasso M., Kostro D., Patiny L., Reymond Jean-Louis (2016), PDB-Explorer: a Web-Based Interactive Map of the Protein Data Bank in Shape Space, in BMC Bioinformatics
, 2015(16), 339.
Awale Mahendra, Reymond Jean-Louis (2015), Similarity Mapplet: Interactive Visualization of the Directory of Useful Decoys and ChEMBL in High Dimensional Chemical Spaces, in Journal of Chemical Information and Modeling
, 55(8), 1509-1516.
Awale Mahendra, Jin Xian, Reymond Jean-Louis (2015), Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints, in Journal of Cheminformatics
, 7(3), 1-15.
Reymond Jean-Louis (2015), The Chemical Space Project, in Accouts of Chemical Research
, 48(3), 722-730.
Kouri Tina M., Awale Mahendra, Slyby James K., Reymond Jean-Louis, Mehta Dinesh P. (2014), “Social” Network of Isomers Based on Bond Count Distance: Algorithms, in Journal of Chemical Information and Modeling
, 54(1), 57-68.
Awale Mahendra, Reymond Jean-Louis (2014), A multi-fingerprint browser for the ZINC database, in Nucleic Acids Research
Awale Mahendra, Reymond Jean-Louis (2014), Atom Pair 2D-Fingerprints Perceive 3D-Molecular Shape and Pharmacophores for Very Fast Virtual Screening of ZINC and GDB-17, in Journal of Chemical Information and Modeling
, 54(7), 1892-1907.
Reymond Jean-Louis, Ruddigkeit Lars, Awale Mahendra, Jacoby Ed. E. (2014), Considerations on the Drug-Like Chemical Space, in Jacoby E. (ed.), Pan Standford Publishing, Singapore, 39-64.
Bürgi Justus, Awale Mahendra, Boss Silvan D., Schaer Tifany, Marger Fabrice, Viveros-Paredes Juan M., Bertrand Sonia, Gertsch Jürg, Bertrand Daniel, Reymond Jean-Louis (2014), Discovery of Potent Positive Allosteric Modulators of the α3β2 Nicotinic Acetylcholine Receptor by a Chemical Space Walk in ChEMBL, in ACS Chemical Neuroscience
, 5(5), 346-359.
Ruddigkeit Lars, Awale Mahendra, Reymond Jean-Louis (2014), Expanding the fragrance chemical space for virtual screening, in Journal of Cheminformatics
, 6(27), 1-12.
Ruddigkeit Lars, Reymond Jean-Louis, Martinez-Mayorga Ed. K., Medina-Franco J.L. (2014), The Chemical Space of Flavours, in Martinez-Mayorga Ed. K. (ed.), 83-96.
Schwartz Julian, Awale Mahendra, Reymond Jean-Louis (2013), Article Previous Article Next Article Table of Contents SMIfp (SMILES fingerprint) Chemical Space for Virtual Screening and Visualization of Large Databases of Organic Molecules, in Journal of Chemical Information and Modeling
, 53(8), 1979-1989.
Awale Mahendra, van Deursen Ruud, Reymond Jean-Louis (2013), MQN-Mapplet: Visualization of Chemical Space with Interactive Maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13, in Journal of Chemical Information and Modeling
, 53(2), 509-518.
Ruddigkeit Lars, Blum Lorenz C., Reymond Jean-Louis (2013), Visualization and Virtual Screening of the Chemical Universe Database GDB-17, in Journal of Chemical Information and Modeling
, 53(1), 56-65.
The continuous discovery of new small molecule drugs is essential to the success of modern medicine, in particular to address unmet medical needs, to combat emerging infectious diseases, and to improve existing therapies. Recently, it has become increasingly difficult to develop such new drugs, largely due to lack of efficacy, side effects and toxicity issues. These difficulties have raised the attention to the problem of carefully designing drugs taking multiple parameters into accounts, and have spurred the development of computer-aided drug design as key discipline to support drug discovery. Part of these efforts are devoted to de novo drug design, an approach which aims to select molecules by virtual screening (VS) to focus efforts on the most promising compounds and increase productivity. We have contributed to this field by enumerating the Chemical Universe Databases, which list all organic molecules that are possible following simple rules of chemical stability and synthetic feasibility, and represent an extremely vast reservoir of potential new drugs. In this proposal, we will expand our exploration of chemical space in search for new drugs in three projects addressing enumeration and VS methodology and their application in drug discovery.