Combining the Classification and Pharmacophore Approaches to Understand Homogeneous Olfactory Perceptions at Peripheral Level: Focus on Two Aroma Mixtures
Abstract
:1. Introduction
- An odor blending, which results from a configural processing of the mixture and occurs when the perceived odor is a new odor that differs from those of the odorants in the mixture;
- A complete overshadowing (or masking) when the odor of only one of the components of the mixture is recognized.
2. Results
2.1. Overview of the Dataset
2.2. Dimensions Reduction and Clustering
2.2.1. Dimensions Reduction
2.2.2. Clustering
2.3. Distribution of Odor Notes within Clusters
- the relative frequency of every odor notes compared to its frequency in the database (Equation (1));
- the relative frequency of odorants carrying each odor note compared to the number of molecules in the considered cluster (Equation (2)).
2.4. Co-Occurrences of Odor Notes across the Clusters SOM16
2.5. Selection of Subsets of Odorants Based on Odor Profiles
- If in these first criteria, more than 10 molecules were selected, we again selected these molecules in which the percentage of noncommon odor notes was the smallest;
- If there was still a need to restrict the number of molecules selected, we selected the molecules that had the highest percentage of common odor notes.
2.6. Pharmacophore Study
- From groups based on the mixture components and containing at least two molecules of the mixtures;
- From each molecule component of the mixtures: each molecule is, in fact, an ensemble of its conformers (energy range of 21 kJ/mol) and was denoted “M-c”, where M is the molecule, and c symbolizes conformers;
- From the subsets of molecules selected in the SOM16 clusters: the subsets of various molecules were named by the initial of the referred molecule followed by the initial “s” (for subset). For example, the vanillin subset selected on the basis of the odorant profile was named “V-s”.
2.6.1. Pharmacophores Generated from Subsets Composed of Components of the Mixtures
- Pharmacophores generated from the subsets based on the “Red Cordial” mixture
- 2.
- Pharmacophores generated from the subset WL/IA-s
2.6.2. Pharmacophore Generated from the Conformers of Each Single Molecule Component of the RC Mixture and WL/IA Masking
2.6.3. Pharmacophores from the Subsets of Molecules Having Similar Odor Profiles
2.6.4. Pharmacophore Comparisons
- The hypotheses generated from the molecules: hyp-V-c, hyp-IA-c, F, and hyp-WL-c;
- The hypotheses generated from the subsets of molecules having odor profiles similar to those of components of the mixtures: hyp-V-s, hyp-IA-s, hyp-F-s, and hyp-WL-s;
- The hypothesis of each molecule with the hypothesis generated from the subset of similar odor profiles.
3. Discussion
4. Materials and Methods
4.1. Description of the Dataset and Molecules of Interest
4.2. Fingerprint Generation, Dimension Reduction and Clustering
4.3. Construction of Pharmacophores
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
Appendix A
Appendix A.1. Classification at Level L4
- In area Aa: 1547 elements constitute the clusters k-means4-Cl-3 and SOM4-Cl-3.
- In area Ab: 1569 elements constitute the clusters k-means4-Cl-4 and SOM4-Cl-2.
- The area Ac encloses the following clusters: k-means4-Cl-1 (932 elements), k-means4-Cl-2 (1617elements), SOM4-Cl-1 (1612) and SOM4-Cl-4 (937 elements).
Appendix A.2. Classification at Level L9
- k-means9-Cl-3 (394 elements), k-means9-Cl-4 (575 elements), k-means9-Cl-8 (569 elements);
- SOM9-Cl-7 (933 elements) and SOM9-Cl-8 (605 elements).
- To the clusters k-means9-Cl-1 (377 elements), k-means9-Cl-5 (1249 elements) and k-means9-Cl-9 (917 elements);
- To the clusters SOM9-Cl-2 (377 elements), SOM9-Cl-1 (1248 elements) and SOM9-Cl-3 (918 elements).
Appendix A.3. Classification at Level L16
k-means16 ∩ SOM16 | Number of Elements |
---|---|
k-means16-Cl-8 ∩ SOM16-Cl-2 | 499 |
k-means16-Cl-8 ∩ SOM16-Cl-5 | 400 |
k-means16-Cl-8 ∩ SOM16-Cl-6 | 130 |
k-means16-Cl-11 ∩ SOM16-Cl-1 | 430 |
k-means16-Cl-11 ∩ SOM16-Cl-2 | 88 |
Clusters in Area Ac | Number of Elements |
---|---|
k-means16-Cl-1 | 185 |
k-means16-Cl-2 | 248 |
k-means16-Cl-3 | 250 |
k-means16-Cl-4 | 608 |
k-means16-Cl-5 | 302 |
k-means16-Cl-6 | 146 |
k-means16-Cl-9 | 266 |
k-means16-Cl-10 | 145 |
k-means16-Cl-12 | 270 |
k-means16-Cl-13 | 123 |
SOM16-Cl-10 | 145 |
SOM16-Cl-11 | 252 |
SOM16-Cl-13 | 629 |
SOM16-Cl-14 | 686 |
SOM16-Cl-15 | 496 |
SOM16-Cl-16 | 335 |
k-means16 ∩ SOM16 | Number of Elements |
---|---|
k-means16-Cl-1 ∩ SOM16-Cl-16 | 185 |
k-means16-Cl-2 ∩ SOM16-Cl-11 | 248 |
k-means16-Cl-3 ∩ SOM16-Cl-13 | 250 |
k-means16-Cl-4 ∩ SOM16-Cl-13 | 379 |
k-means16-Cl-4 ∩ SOM16-Cl-14 | 229 |
k-means16-Cl-5 ∩ SOM16-Cl-11 | 4 |
k-means16-Cl-5 ∩ SOM16-Cl-15 | 298 |
k-means16-Cl-6 ∩ SOM16-Cl-14 | 146 |
k-means16-Cl-9 ∩ SOM16-Cl-15 | 197 |
k-means16-Cl-9 ∩ SOM16-Cl-16 | 69 |
k-means16-Cl-10 ∩ SOM16-Cl-10 | 145 |
k-means16-Cl-12 ∩ SOM16-Cl-14 | 269 |
k-means16-Cl-12 ∩ SOM16-Cl-15 | 1 |
k-means16-Cl-13 ∩ SOM16-Cl-14 | 42 |
k-means16-Cl-13 ∩ SOM16-Cl-16 | 81 |
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Name | CAS | Odor Notes |
---|---|---|
Vanillin | 121-33-5 | Sweet; vanilla; creamy; chocolate |
Isoamyl acetate 1 | 123-92-2 | Sweet; fruity; banana; solvent; pear |
Frambinone | 5471-51-2 | Sweet; berry; raspberry; ripe; floral; fruity |
Ethyl acetate | 141-78-6 | Ethereal; fruity; sweet; weedy; green; sharp; brandy; winey |
beta-Damascenone | 23696-85-7 | Fruity; floral; apple; plum; tea; rose; tobacco; natural; grape; raspberry; sweet |
beta-Ionone | 14901-07-6 | Floral; woody; sweet; fruity; berry; tropical; violet; raspberry; dry; powdery orris |
Whiskey lactone | 39212-23-2 | Tonka; coumarinic; coconut; toasted; nutty; celery; burnt; woody; lactonic; maple 2; lovage 2 |
Name | Area | k-means4 | k-means9 | k-means16 | SOM4 | SOM9 | SOM16 |
---|---|---|---|---|---|---|---|
Vanillin | Ab | 3 | 2 | 8 | 3 | 9 | 2 |
Isoamyl acetate | Ac | 1 | 9 | 4 | 4 | 3 | 13 |
Frambinone | Ab | 3 | 2 | 8 | 3 | 9 | 5 |
Ethyl acetate | Ac | 1 | 9 | 4 | 4 | 3 | 14 |
beta-Ionone | Aa | 4 | 8 | 7 | 2 | 7 | 8 |
beta-Damascenone | Aa | 4 | 8 | 7 | 2 | 7 | 8 |
Whiskey lactone | Aa | 4 | 4 | 16 | 2 | 8 | 4 |
Cluster | Molecule of Interest | Molecule’s Subset with Similar Odor Profile |
---|---|---|
SOM16-Cl-2 | Vanillin | Vanillyl isobutyrate; vanillin propylene glycol acetal; ethyl vanillin isobutyrate; 1-Ethoxy-2-methoxybenzene; ortho-dimethyl hydroquinone; ethyl vanillin; vanillyl acetate; vanillylidene acetone; vanillin hexylene glycol acetal; ethyl vanillin hexylene glycol acetal; ethyl vanillin propylene glycol acetal |
SOM16-Cl-4 | Whiskey lactone | 7-Methyltetrahydronaphthalenone; delta-Heptalactone; Menthofurolactone; Octahydrocoumarin; Laitone; Coconut naphthalenone; (R)-tonka furanone; (+/−)-dihydromint lactone |
SOM16-Cl-5 | Frambinone | Anisyl isobutyrate; 4-hydroxyphenethyl alcohol; 4-(para-tolyl)-2-butanone; Tufurol acetate; 2-Methylbenzyl acetate; alpha-Methylbenzyl-propionate; Phenethyl-2-methylbutyrate; methyl 4-phenyl butyrate; benzyl acetoacetate |
SOM16-Cl-8 | beta-Ionone | beta-ionyl acetate; alpha-ionol; alpha-ionyl acetate; 3-Methylcyclohexyl acetate; beta-Irone; Campholene-acetate; Nopyl-acetate; 4-dimethyl ionone |
SOM16-Cl-8 | beta-Damascenone | plum damascone (high alpha); (Z)-alpha-damascone; Cyclohexylethyl isovalerate; Cyclohexylethyl valerate; 1-(3-(methyl thio)-butyryl)-2,6,6-trimethyl cyclohexene; 3-cyclohexene-1-carboxylic acid, 2,6,6-trimethyl-, methyl ester |
SOM16-Cl-13 | Isoamyl acetate | 2-Methylbutyl-butyrate; hexyl acetate; isobutyl propionate; methyl butyrate; isopropyl propionate; methyl 4-methyl valerate; isoamyl butyrate; propyl acetate; butyl acetate; amyl acetate |
SOM16-Cl-14 | Ethyl acetate | 2-Methylbut-2-enyl-formate; Isobutyl pyruvate; methyl acetate; methyl (E)-2-butenoate; ethyl 2-methyl butyrate; 2-methyl butyl propionate; isopropyl acetate; ethyl nitrite; hexyl lactate; methyl 3-hydroxybutyrate |
Pair of Hypotheses | RMSD |
---|---|
hyp-V-c and hyp-IA-c | 0.5647 |
hyp-V-c and hyp-F-c | - |
hyp-IA-c and hyp-F-c | - |
hyp-WL-c and hyp-IA-c | 0.1485 |
hyp-V-s and hyp-IA-s | 0.5305 |
hyp-V-s and hyp-F-s | 1.3647 |
hyp-IA-s and hyp-F-s | 0.7449 |
hyp-WL-s and hyp-IA-s | 0.3842 |
hyp-V-c and hyp-V-s | 0.066 |
hyp-IA-c and hyp-IA-s | 0.247 |
hyp-F-c and hyp-F-s | - |
hyp-WL-c and hyp-WL-s | 0.442 |
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Rugard, M.; Audouze, K.; Tromelin, A. Combining the Classification and Pharmacophore Approaches to Understand Homogeneous Olfactory Perceptions at Peripheral Level: Focus on Two Aroma Mixtures. Molecules 2023, 28, 4028. https://doi.org/10.3390/molecules28104028
Rugard M, Audouze K, Tromelin A. Combining the Classification and Pharmacophore Approaches to Understand Homogeneous Olfactory Perceptions at Peripheral Level: Focus on Two Aroma Mixtures. Molecules. 2023; 28(10):4028. https://doi.org/10.3390/molecules28104028
Chicago/Turabian StyleRugard, Marylène, Karine Audouze, and Anne Tromelin. 2023. "Combining the Classification and Pharmacophore Approaches to Understand Homogeneous Olfactory Perceptions at Peripheral Level: Focus on Two Aroma Mixtures" Molecules 28, no. 10: 4028. https://doi.org/10.3390/molecules28104028