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Ollitrault G, Achebouche R, Dreux A, Murail S, Audouze K, Tromelin A, Taboureau O. Pred-O3, a web server to predict molecules, olfactory receptors and odor relationships. Nucleic Acids Res 2024:gkae305. [PMID: 38661190 DOI: 10.1093/nar/gkae305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/04/2024] [Accepted: 04/23/2024] [Indexed: 04/26/2024] Open
Abstract
The sense of smell is a biological process involving volatile molecules that interact with proteins called olfactory receptors to transmit a nervous message that allows the recognition of a perceived odor. However, the relationships between odorant molecules, olfactory receptors and odors (O3) are far from being well understood due to the combinatorial olfactory codes and large family of olfactory receptors. This is the reason why, based on 5802 odorant molecules and their annotations to 863 olfactory receptors (human) and 7029 odors and flavors annotations, a web server called Pred-O3 has been designed to provide insights into olfaction. Predictive models based on Artificial Intelligence have been developed allowing to suggest olfactory receptors and odors associated with a new molecule. In addition, based on the encoding of the odorant molecule's structure, physicochemical features related to odors and/or olfactory receptors are proposed. Finally, based on the structural models of the 98 olfactory receptors a systematic docking protocol can be applied and suggest if a molecule can bind or not to an olfactory receptor. Therefore, Pred-O3 is well suited to aid in the design of new odorant molecules and assist in fragrance research and sensory neuroscience. Pred-O3 is accessible at ' https://odor.rpbs.univ-paris-diderot.fr/'.
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Affiliation(s)
| | | | - Antoine Dreux
- Inserm U1133, CNRS UMR 8251, Université Paris Cité, Paris, France
| | - Samuel Murail
- Inserm U1133, CNRS UMR 8251, Université Paris Cité, Paris, France
| | | | - Anne Tromelin
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Institut Agro, Université de Bourgogne, F-21000 Dijon, France
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Sharma A, Kumar R, Varadwaj P. Developing human olfactory network and exploring olfactory receptor-odorant interaction. J Biomol Struct Dyn 2023; 41:8941-8960. [PMID: 36310099 DOI: 10.1080/07391102.2022.2138976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
The Olfactory receptor (OR)-odorant interactions are perplexed. ORs can bind to structurally diverse odorants associated with one or more odor percepts. Various attempts have been made to understand the intricacies of OR-odorant interaction. In this study, experimentally documented OR-odorant interactions are investigated comprehensively to; (a) suggest potential odor percepts for ORs based on the OR-OR network; (b) determine how odorants interacting with specific ORs differ in terms of inherent pharmacophoric features and molecular properties, (c) identify molecular interactions that explained OR-odorant interactions of selective ORs; and (d) predict the probable role of ORs other than olfaction. Human olfactory receptor network (hORnet) is developed to study possible odor percepts for ORs. We identified six molecular properties which showed variation and significant patterns to differentiate odorants binding with five ORs. The pharmacophore analysis revealed that odorants subset of five ORs follow similar pharmacophore hypothesis, (one hydrogen acceptor and two hydrophobic regions) but differ in terms of distance and orientation of pharmacophoric features. To ascertain the binding site residues and key interactions between the selected ORs and their interacting odorants, 3D-structure modelling, docking and molecular dynamics studies were carried out. Lastly, the potential role of ORs beyond olfaction is explored. A human OR-OR network was developed to suggest possible odor percepts for ORs using empirically proven OR-odorant interactions. We sought to find out significant characteristics, molecular properties, and molecular interactions that could explain OR-odorant interactions and add to the understanding of the complex issue of odor perception.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anju Sharma
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, Uttar Pradesh, India
| | - Rajnish Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, Uttar Pradesh, India
| | - Pritish Varadwaj
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, Uttar Pradesh, India
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McCabe AK, Keyes JK, Hemetsberger H, Kurr CV, Albright B, Ward MG, McKinley ML, Breezley SJ, Cole CA. Aroma Profile Development in Beer Fermented with Azacca, Idaho-7, and Sultana Hops. Molecules 2023; 28:5802. [PMID: 37570773 PMCID: PMC10421000 DOI: 10.3390/molecules28155802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Hops are among the most costly and environmentally impactful raw materials used in brewing, yet they play a crucial role in the aroma of beer. However, predicting beer aroma based on hop variety or hopping method remains arduous. This is partly because hop oils are unique for each hop variety, and they may be biotransformed by yeast enzymes during fermentation. Even slight molecular structure modifications can dramatically affect the organoleptic properties of beer. Through combined chemical and sensory analysis of dry-hopped beers prepared with different hop varieties (Azacca, Idaho-7, and Sultana), this work aimed to profile the aromas and the overall biotransformation processes taking place during fermentation. A total of 51 volatile organic compounds (VOCs) were semi-quantified and monitored: 19 esters, 13 sesquiterpenes, 7 ketones, 7 alcohols, 4 monoterpenes, and 1 volatile acid. There were significant similarities in the measured analytes and perceived aromas of these beers, but one hop variety (Sultana) delivered an increased quantity of unique aromas and an increased concentration of volatiles in the headspace for the same quantity of hop pellets added. This work provides practical information to brewers who utilize hops in beer production.
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Affiliation(s)
- Anna K. McCabe
- Department of Chemistry & Biochemistry, Fort Lewis College, 1000 Rim Drive, Durango, CO 81301, USA; (A.K.M.); (J.K.K.); (M.G.W.); (M.L.M.)
| | - Jasmine K. Keyes
- Department of Chemistry & Biochemistry, Fort Lewis College, 1000 Rim Drive, Durango, CO 81301, USA; (A.K.M.); (J.K.K.); (M.G.W.); (M.L.M.)
| | - Heidi Hemetsberger
- Ska Brewing Company, 225 Girard St., Durango, CO 81303, USA; (H.H.); (C.V.K.); (B.A.); (S.J.B.)
| | - Chris V. Kurr
- Ska Brewing Company, 225 Girard St., Durango, CO 81303, USA; (H.H.); (C.V.K.); (B.A.); (S.J.B.)
| | - Bryan Albright
- Ska Brewing Company, 225 Girard St., Durango, CO 81303, USA; (H.H.); (C.V.K.); (B.A.); (S.J.B.)
| | - Michael G. Ward
- Department of Chemistry & Biochemistry, Fort Lewis College, 1000 Rim Drive, Durango, CO 81301, USA; (A.K.M.); (J.K.K.); (M.G.W.); (M.L.M.)
| | - Megan L. McKinley
- Department of Chemistry & Biochemistry, Fort Lewis College, 1000 Rim Drive, Durango, CO 81301, USA; (A.K.M.); (J.K.K.); (M.G.W.); (M.L.M.)
| | - Steven J. Breezley
- Ska Brewing Company, 225 Girard St., Durango, CO 81303, USA; (H.H.); (C.V.K.); (B.A.); (S.J.B.)
| | - Callie A. Cole
- Department of Chemistry & Biochemistry, Fort Lewis College, 1000 Rim Drive, Durango, CO 81301, USA; (A.K.M.); (J.K.K.); (M.G.W.); (M.L.M.)
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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:molecules28104028. [PMID: 37241770 DOI: 10.3390/molecules28104028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/20/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
The mechanisms involved in the homogeneous perception of odorant mixtures remain largely unknown. With the aim of enhancing knowledge about blending and masking mixture perceptions, we focused on structure-odor relationships by combining the classification and pharmacophore approaches. We built a dataset of about 5000 molecules and their related odors and reduced the multidimensional space defined by 1014 fingerprints representing the structures to a tridimensional 3D space using uniform manifold approximation and projection (UMAP). The self-organizing map (SOM) classification was then performed using the 3D coordinates in the UMAP space that defined specific clusters. We explored the allocating in these clusters of the components of two aroma mixtures: a blended mixture (red cordial (RC) mixture, 6 molecules) and a masking binary mixture (isoamyl acetate/whiskey-lactone [IA/WL]). Focusing on clusters containing the components of the mixtures, we looked at the odor notes carried by the molecules belonging to these clusters and also at their structural features by pharmacophore modeling (PHASE). The obtained pharmacophore models suggest that WL and IA could have a common binding site(s) at the peripheral level, but that would be excluded for the components of RC. In vitro experiments will soon be carried out to assess these hypotheses.
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Affiliation(s)
- Marylène Rugard
- T3S, Inserm UMR S-1124, Université Paris Cité, F-75006 Paris, France
| | - Karine Audouze
- T3S, Inserm UMR S-1124, Université Paris Cité, F-75006 Paris, France
| | - Anne Tromelin
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Institut Agro, Université de Bourgogne, F-21000 Dijon, France
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Analysis of the Ability to Produce Pleasant Aromas on Sour Whey and Buttermilk By-Products by Mold Galactomyces geotrichum: Identification of Key Odorants. Molecules 2021; 26:molecules26206239. [PMID: 34684821 PMCID: PMC8537768 DOI: 10.3390/molecules26206239] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 11/20/2022] Open
Abstract
Currently, there is a growing demand for flavorings, especially of natural origin. It is worth paying attention to the biotechnological processes of flavor production, characterized by simplicity, high efficiency and relatively low cost. In this study, we analyzed the ability of the Galac tomyces geotrichum mold to transform by-products of the dairy industry: sour whey and buttermilk to complex flavour mixtures with pleasant, honey-rose aroma. Furthermore, the aroma complexity of the fermentation product has been carefully identified applying a sensomic approach involving the use of gas chromatography-olfactometry (GC-O), gas chromatography-mass spectrometry (GC-MS) and stable isotope dilution assay (SIDA) to identify and quantify aroma compounds. Based on the calculation of odor activity value (OAV), 13 key aroma compounds were present in both tested variants. The highest OAVs were found for phenylacetaldehyde (honey-like) in the buttermilk variant (912) and 2-phenylethanol (rose-like) in the sour whey variant (524). High values of this indicator were also recorded for phenylacetaldehyde (319) and 3-methyl-1-butanol with a fruity aroma (149) in the sour whey culture. The other compounds identified are 3-methylbutanal (malty), 2,3-butanedione (cheesy), isovaleric acid (cheesy), 3-(methylthio)-propanal (boiled potato), butanoic acid (vinegar), (E)-2-nonenal (fatty), ethyl furaneol (burnt sugar), dimethyl trisulfide (cabbage), and acetic acid (vinegar).
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Malfeito-Ferreira M. Fine wine flavour perception and appreciation: Blending neuronal processes, tasting methods and expertise. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.06.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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