Medicinal Chemistry Aware Database GDBMedChem

Awale, Mahendra; Sirockin, Finton; Stiefl, Nikolaus; Reymond, Jean-Louis (2019). Medicinal Chemistry Aware Database GDBMedChem. Molecular informatics, 38(8-9), p. 1900031. Wiley 10.1002/minf.201900031

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The generated database GDB17 enumerates 166.4 billion possible molecules up to 17 atoms of C, N, O, S and halogens following simple chemical stability and synthetic feasibility rules, however medicinal chemistry criteria are not taken into account. Here we applied rules inspired by medicinal chemistry to exclude problematic functional groups and complex molecules from GDB17, and sampled the resulting subset uniformly across molecular size, stereochemistry and polarity to form GDBMedChem as a compact collection of 10 million small molecules. This collection has reduced complexity and better synthetic accessibility than the entire GDB17 but retains higher sp3‐carbon fraction and natural product likeness scores compared to known drugs. GDBMedChem molecules are more diverse and very different from known molecules in terms of substructures and represent an unprecedented source of diversity for drug design. GDBMedChem is available for 3D‐visualization, similarity searching and for download at http://gdb.unibe.ch.

Item Type:

Journal Article (Original Article)

Division/Institute:

08 Faculty of Science > Departement of Chemistry and Biochemistry

UniBE Contributor:

Awale, Mahendra and Reymond, Jean-Louis

Subjects:

500 Science > 570 Life sciences; biology
500 Science > 540 Chemistry

ISSN:

1868-1743

Publisher:

Wiley

Language:

English

Submitter:

Sandra Tanja Zbinden Di Biase

Date Deposited:

23 Jan 2020 10:05

Last Modified:

23 Jan 2020 10:14

Publisher DOI:

10.1002/minf.201900031

PubMed ID:

31169974

BORIS DOI:

10.7892/boris.138464

URI:

https://boris.unibe.ch/id/eprint/138464

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