Table 1.
List of odorants used in the docking analysis.
The odorants have been classified based on their functional groups. Odorants which are known to bind to insect ORs are listed separately. There are two odorants specific to ORs from model organisms C. elegans (odr-10) and M. musculus (mOR-EG). Repellents were chosen for clustering along with the odorants (based on chemical similarity) to understand their similarity to the odorants.
Fig 1.
GRID selected for Induced Fit Docking.
Induced Fit docking protocol was standardized using the experimental data available on mouse ORs that responds to eugenol (mOR-EG). Different grid parameters and constraints were used to standardize the protocol as shown in Table 2. The use of the upper half of the receptor facing the extracellular milieu gave the best score for eugenol binding as compared to the other parameters. Thus similar grid parameters were used for all the IFD runs. The receptor TM helices 1–7 are coloured in VIBGYOR colour (Violet, Indigo, Blue, Green, Yellow, Orange and Red). Figure has been generated using PYMOL (The PyMOL Molecular Graphics System, Version 1.5.0.4 Schrödinger, LLC).
Fig 2.
This figure represents the methodology followed for Induced Fit Docking. Ten pairs of human-mouse ORs were used as receptors and the 125 odorants as ligands and IFD was carried out using XP scoring. The odor profile for all the receptors obtained using IFD has been represented as heat map (Fig 8).
Table 2.
The different parameters used for standardization of IFD protocol.
Parameter 5 (marked in bold) shows the highest score for binding of known agonist, eugenol to mOR-EG. Parameter 5 was thus chosen for further IFD analysis.
Fig 3.
The binding mode of eugenol to mOR-EG.
The figure shows the binding site of eugenol to mOR-EG. Phe 182 residue forms a H-bond with the—OH group. Other interacting residues are Tyr 260 and Asn 264, while other residues contribute to the hydrophobic pocket required for odorant binding. The figure is obtained using the “Ligand Interaction Diagram” of the GLIDE software (Schrödinger Release 2013–1:, version 2.6, Schrödinger, LLC, New York, NY, 2013).
Fig 4.
The number of common odorants among the best ten high scoring odorants for 10 human-mouse OR pairs.
The figure shows the number of common ligands picked by ten OR pairs. The OR pair with highest sequence identity (Pair 2) has 4 common ligands while OR pair 5 and 10 have eight common ligands. The sequence identity of each pair is marked on top of the bar in the graph.
Fig 5.
Odorant (Helional) binding residues of OR pair 2.
(a): The odorant binding residues of human OR1A1. (b): The odorant binding residues of mouse OR18480066. The residues circled in red are the ones that are equivalent (identical) to both human and mouse ORs. The variability in the binding site results in differential responses and orientation of ligand binding of the two closely related ORs to the given odorant. The figure is obtained using the “Ligand Interaction Diagram” of the GLIDE software (Schrödinger Release 2013–1: version 2.6, Schrödinger, LLC, New York, NY, 2013) and PyMOL (The PyMOL Molecular Graphics System, Version 1.5.0.4 Schrödinger, LLC).
Table 3.
The receptor dataset used for the IFD study.
The table shows the list of human and mouse ORs used for IFD analysis. Both the common name and GI ID of each OR is mentioned. The OR pair 2 has the maximum sequence identity of 84%. The orthologous pairs of ORs have been marked with an asterix '*'.
Table 4.
The first ten high scoring ligands for human-mouse OR pair 2.
The human-mouse OR pair 2 has the maximum sequence identity of 84%. The highest scoring ligand is Helional for the two ORs, while there are only 4 common ligands out of the ten high scoring ligands (shown in bold font). The ligands that are dissimilar are from different clusters in ligand clustering analysis (Column 3 and 6).
Fig 6.
The distribution of odorants (125) into different chemical classes.
The odorants belonged to different chemical classes with varying length of carbon chains. Few specific odorants that induce responses from insect ORs and mammalian ORs were grouped separately to understand their receptor binding activity.
Fig 7.
The distribution of MOLPRINT2D features of the odorants.
(a) shows the range of molecular weight of the odorants. Most of the odorants have a molecular weight between 100–150 Daltons. (b) shows the number of rotatable bonds present in the given set of odorants. The number of rotatable bonds varies from 1 to 11. (c) shows the number of aromatic rings present in the odorants. 80% of the odorants are aliphatic. (d) and (e) show the number of hydrogen bond acceptors and donor atoms respectively in the odorants. There are a maximum of 5 hydrogen bond acceptors and 3 hydrogen bond donor atom in the odorants.
Table 5.
The different merging distances used for clustering of ligands.
The ligand clusters obtained at a merging distance of 0.85 shows the presence of highly similar ligands in a given cluster and thus has been used for further analysis.
Table 6.
The number of ligands in each of the 36 ligand clusters obtained by clustering (as mentioned in methods).
Cluster 33 has 55 aliphatic odorant members in it and thus it is further subdivided into 11 subclusters based on functional groups of the odorants.
Fig 8.
Heat map of the odorant profile of 10 human-mouse OR pairs.
X-axis shows the human-mouse OR pair and the sequence identity between human-mouse OR pairs. Y-axis indicates the number of 130 odorants used in this study. The heat map is obtained using the gscore (kcal/mol) of interaction of each ligand to the given receptor. The scores have been normalized between 0 to 1 as shown in the scale. The odorants for which experimental data are available (Steroids, Helional, Undecanal, Eugenol and Citronellol) have been marked with a red arrow. Insect ORs have been marked in a green rectangular box. The heat map has been generated using R software.
Table 7.
Average difference in binding energies (kcal/mol) of odorants to 10 human-mouse OR pairs.
The average binding energies of 125 odorants to each of the ORs were calculated and the difference in the average energy between each human-mouse OR pair has been reported. The OR pair 2 (with the highest sequence identity of 84%) has the minimum difference in binding energy.
Table 8.
The ten high scoring odorants for mOR-EG.
Helional, Ethyl-vanillin and Eugenol are the experimentally proven ligands for mOR-EG which occur among the top five best scoring odorant-receptor interactions.
Table 9.
OR-odorant interactions reported till date.
The OR-odorant interactions reported in studies done so far has been mentioned in this table. The remarks column indicates the results from the current study that correspond to the known data on OR-odorant interactions.
Fig 9.
Binding mode of Helional and (-) Citronellol to human OR1A1.
Helional (a) forms three hydrogen bonds and one salt bridge with the residues of OR1A1, while Citronellol (b) forms only one H-bond with the residues of OR. Helional is known to be the most potent alcohol for human ORs. The figure is obtained using the “Ligand Interaction Diagram” of the GLIDE software (Schrödinger Release 2013–1:, version 2.6, Schrödinger, LLC, New York, NY, 2013).
Fig 10.
Binding mode of bourgeonal to human OR1D2.
Bourgeonal is known to be the most potent ligand of human OR1D2. It forms a H-bond with the residue Phe168 of the receptor. It binds to the common GPCR binding pocket formed by TM3, 4, 5 and 7. The figure is obtained using the “Ligand Interaction Diagram” of the GLIDE software (Schrödinger Release 2013–1:, version 2.6, Schrödinger, LLC, New York, NY, 2013).
Fig 11.
Binding mode of androstenone (agonist) and undecanal (antagonist) to the human olfactory receptor 1D2.
Both the odorants bind in the same binding pocket but interact with different residues. Val108, Val 109, Phe 168, Ile 187, Ser 230, Tyr 233 and Gly 234 are the common residues at the binding site. The figure is obtained using the “Ligand Interaction Diagram” of the GLIDE software (Schrödinger Release 2013–1:, version 2.6, Schrödinger, LLC, New York, NY, 2013).
Fig 12.
Best binding mode of Helional to OR.
This interaction has the highest score in the IFD runs. There are three H-bonds and one salt bridge interaction between the odorant and the residues of the olfactory receptor. The figure is obtained using the “Ligand Interaction Diagram” of the GLIDE software (Schrödinger Release 2013–1:, version 2.6, Schrödinger, LLC, New York, NY, 2013).
Table 10.
Average gscore (kcal/mol) for interactions between aldehydes in the odorant dataset to the 10 human-mouse OR pairs.
The average binding energy of each of the aldehyde to the 20 ORs was calculated. Helional is known to be the most potent aldehyde as compared to aldehydes with 5–10 carbon atoms.