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Cheminformatics Analysis of Organic Substituents: Identification of the Most Common Substituents, Calculation of Substituent Properties, and Automatic Identification of Drug-like Bioisosteric Groups
Abstract
A large set of more than 3 million molecules was processed to find all the organic substituents contained in the set and to identify the most common ones. During the analysis, 849 574 unique substituents were found. Extrapolated to the number of known organic molecules, this result suggests that about 3.1 million substituents are known. Based on these findings the size of virtual organic chemistry space accessible using currently known synthetic methods is estimated to be between 10(20) and 10(24) molecules. The extracted substituents were characterized by calculated electronic, hydrophobic, steric, and hydrogen bonding properties as well as by the drug-likeness index. Various possible applications of such a large database of drug-like substituents characterized by calculated properties are discussed and illustrated by reference to a Web-based tool for automatic identification of bioisosteric groups.
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Cited by
Ertl, P., & Schuffenhauer, A. (2009) · Journal of Cheminformatics · doi:10.1186/1758-2946-1-8 · Cited by 1,939
Self-citationUltra-large library docking for discovering new chemotypes
Lyu, J., Wang, S., Balius, T. E., Singh, I., Levit, A., Moroz, Y. S., O’Meara, M. J., Che, T., Algaa, E., Tolmachova, K., et al. (2019) · Nature · doi:10.1038/s41586-019-0917-9 · Cited by 998
Reymond, J.-L. (2015) · Accounts of Chemical Research · doi:10.1021/ar500432k · Cited by 720
Estimation of the size of drug-like chemical space based on GDB-17 data
Polishchuk, P. G., Madzhidov, T. I., & Varnek, A. (2013) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-013-9672-4 · Cited by 619
Fragment-Based Approaches in Drug Discovery and Chemical Biology
Scott, D. E., Coyne, A. G., Hudson, S. A., & Abell, C. (2012) · Biochemistry · doi:10.1021/bi3005126 · Cited by 460
Synthon-based ligand discovery in virtual libraries of over 11 billion compounds
Sadybekov, A. A., Sadybekov, A. V., Liu, Y., Iliopoulos-Tsoutsouvas, C., Huang, X.-P., Pickett, J., Houser, B., Patel, N., Tran, N. K., Tong, F., et al. (2022) · Nature · doi:10.1038/s41586-021-04220-9 · Cited by 417
“Standard libraries for high-throughput screening (HTS) 10 and virtual ligand screening (VLS) 11–13 have been historically limited to fewer than 10 million available compounds, which is a small fraction of the enormous chemical space, estimated to be 10 20 to 10 60 drug-like compounds 14,15 .”
BackgroundLu, S.-H., Wu, J. W., Liu, H.-L., Zhao, J.-H., Liu, K.-T., Chuang, C.-K., Lin, H.-Y., Tsai, W.-B., & Ho, Y. (2011) · Journal of Biomedical Science · doi:10.1186/1423-0127-18-8 · Cited by 204
Autonomous Molecular Design: Then and Now
Dimitrov, T., Kreisbeck, C., Becker, J. S., Aspuru-Guzik, A., & Saikin, S. K. (2019) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.9b01226 · Cited by 103
Fragment Informatics and Computational Fragment‐Based Drug Design: An Overview and Update
Sheng, C., & Zhang, W. (2013) · Medicinal Research Reviews · doi:10.1002/med.21255 · Cited by 80
Metadata
- Authors
- Ertl, P.
- Venue
- Journal of Chemical Information and Computer Sciences
- Publisher
- American Chemical Society (ACS)
- Published
- 2002-12-06
- Volume
- 43
- Issue
- 2
- Pages
- 374-380
- ISSN
- 0095-2338 (ISSN-L)
- 1520-5142
- OpenAlex
- W2166478947
- Cited by
- 292
- References
- 0
- FWCI
- 4.55
- Type
- journal article
- Language
- en
- Open access
- closed
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