Nature-informed · 3,040 compounds
NDL-3040 Natural Derivatives Library
A crossover set of natural derivatives, analogs, semi-natural compounds, and mimics — 3,040 members, historically also referred to as NDL-3000.
NDL-3040 (Natural Derivatives Library; historically also referred to as NDL-3000) is a crossover between pure natural molecules and synthetic organic chemistry. The 3,040-compound set elaborates on the structural diversity of natural chemotypes and includes natural derivatives, analogs, semi-natural compounds, and mimics. Natural chemistry often occupies chemical space distinct from common bioactive and organic molecules, which can help against challenging or emerging targets.
NDL is designed as a structural complement to NPL-800. The two collections are independent and form a useful pair for nature-inspired screening. Available as the full set or custom subsets; vials or 96-/384-well plates.
Chemotype examples listed for the collection include alkaloids, natural phenols, nucleoside analogs, carbohydrates, purines and pyrimidines, flavonoids, steroids, and natural amino acids.
TimTec notes that natural-product scaffolds differ by organism of origin and that NDL includes scaffolds associated with plants, animals, and bacteria (see Ertl & Schuffenhauer, cheminformatics analysis of natural products, Progress in Drug Research, 2008, 66, 217–235).
Literature context cited on the catalog (not TimTec trial data): reviews in J. Med. Chem. 2008 discussing natural products as drug leads (Ojima; Newman) remain the framing TimTec uses for this series.
Published screens that used NDL
Papers below name NDL-3000 (the historical catalog name for this 3,040-compound set). These are literature reports, not TimTec efficacy claims:
- Watson, V. G.; Drake, K. M.; Napper, A. D. Development of a high-throughput screening-compatible assay for the discovery of inhibitors of the AF4-AF9 interaction using AlphaScreen technology. Assay Drug Dev. Technol. 2013. doi:10.1089/adt.2012.495. TimTec NDL = 3,000 natural-product-derived synthetics, screened with NPL.
- Tan, S. Y.; Chua, S. L.; Chen, Y.; Wong, S. C.; Nielsen, T. E.; Givskov, M.; Yang, L.; et al. Identification of five structurally unrelated quorum-sensing inhibitors of Pseudomonas aeruginosa from a natural-derivative database. Antimicrob. Agents Chemother. 2013. doi:10.1128/AAC.00955-13. Structure-based screen of TimTec Natural Derivatives Library (3,040 compounds).
- Chan, J. D.; Day, T. A.; Marchant, J. S. Coalescing beneficial host and deleterious antiparasitic actions as an antischistosomal strategy. eLife 2018, 7:e35755. doi:10.7554/eLife.35755. Screened TimTec NDL-3000 (with NPL-800) as the Natural Derivatives Library.
- Zhang, H.; Pandey, S.; Travers, M.; Sun, H.; et al. Targeting CDK9 reactivates epigenetically silenced genes in cancer. Cell 2018. doi:10.1016/j.cell.2018.09.051. Phenotypic GFP screen of “NDL-3040 natural compound library” purchased from TimTec (3,040 compounds).