ZINC Biogenic Libraries

Biogenic and Biogenic-like libraries in ZINC.

We have created screening libraries based on molecules of biological origin. To be clear, we include both primary metabolites - often just called metabolites - as well as secondary metabolites - often called natural products - in our database of natural products.

Based on Hert et al 2006, we then find all compounds that are similar to these biogenic molecules for the natural product like libraries.

Assembly

• 1. all natural products from public sources. The purchasable version of this is subset 98. ZBS - ZINC Biogenic Subset
• 2. Tanimoto 80% similarity to any Biogenic compound, based on rdkit path-based fingerprints, 2048 bits.
• 3. Fragment Biogenic compounds into Murcko Scaffolds and ring systems (Ertl, via molinspiration). Retain only 10+ atom fragments.
• 3a. Tanimoto 80% similarity (rdkit 2048 pathbased) to any Biogenic fragment in 3 above.
• 3b. Any compound having as a strict substructure the fragments in 3 above.

Results

• organized into lead-like, fragment-like, drug-like, all, and shard-like subsets, for both biogenic and biogenic like. Called ZBG - ZINC BioGenic and ZBL - ZINC Biogenic Like subsets.

Inspiration

inspired by the work of Hert et la. Also Dortmund Group. Also Reses paper.