Abstract
The properties of fragrance molecules in the public databases SuperScent and Flavornet were analyzed to define a “fragrance-like” (FL) property range (Heavy Atom Count ≤ 21, only C, H, O, S, (O + S) ≤ 3, Hydrogen Bond Donor ≤ 1) and the corresponding chemical space including FL molecules from PubChem (NIH repository of molecules), ChEMBL (bioactive molecules), ZINC (drug-like molecules), and GDB-13 (all possible organic molecules up to 13 atoms of C, N, O, S, Cl). The FL subsets of these databases were classified by MQN (Molecular Quantum Numbers, a set of 42 integer value descriptors of molecular structure) and formatted for fast MQN-similarity searching and interactive exploration of color-coded principal component maps in form of the FL-mapplet and FL-browser applications freely available at http://www.gdb.unibe.ch. MQN-similarity is shown to efficiently recover 15 different fragrance molecule families from the different FL subsets, demonstrating the relevance of the MQN-based tool to explore the fragrance chemical space.
Highlights
Fragrance molecules are relatively small, lipophilic and volatile organic compounds that trigger the sense of smell by interacting with olfactory receptor neurons in the upper part of the nose which display a diverse array of olfactory G-protein coupled receptors [1,2,3,4,5,6,7]
Chemical space is understood as the ensemble of all organic molecules in the context of drug discovery, [15,16,17,18,19,20,21,22,23,24,25,26,27] and comprises millions of known molecules collected in public databases such as PubChem, [28] ChemSpider, [29] ZINC, [30]or ChEMBL, [31] and an even much larger number of theoretically possible molecules such as the Chemical Universe Databases GDB-11, [32,33] GDB-13 [34] and GDB-17, [35] listing all
The molecular properties of FragranceDB and TasteDB was analyzed in comparison to PubChem, [26] ChEMBL, [29] ZINC, [28] and GDB-13 [31] as representative databases of the broader chemical space (Table 1)
Summary
Fragrance molecules are relatively small, lipophilic and volatile organic compounds that trigger the sense of smell by interacting with olfactory receptor neurons in the upper part of the nose which display a diverse array of olfactory G-protein coupled receptors [1,2,3,4,5,6,7]. These molecules are essential ingredient in foods, perfumes, soaps, shampoos or lotions, and can be classified according to their perceived smell into tens to hundreds of families [8]. The search for MQN-nearest neighbours is enabled by the FL-browser, which might serve as as a guide to identify new fragrance molecules
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