Molecular docking
Examining the enzymatic capabilities of phyto-constituents through in vitro analysis is ideal. However, this was not feasible due to the exceedingly low concentration of these compounds in the plant extract and the unavailability of certain compounds in the market (Shahid et al., 2023). Consequently, a virtual assessment of these substances can be carried out using molecular docking studies. This approach helps predict the bioactive substances responsible for enzymatic activities. In contemporary drug development, computational techniques like molecular docking play a crucial role. They enable the anticipation and identification of low binding energies and high affinities and provide improved insights into protein-ligand interactions (Shahid et al., 2023).
Plant extracts are recognized for their effectiveness as natural biocides, driving the demand for new drugs. A method called docking is employed to predict potential drugs, which allows for a detailed exploration of the interactions between a ligand and the target protein. Schrodinger, for instance, conducts grid-based ligand docking with energetics to search for favorable interactions between small ligand molecules and larger receptor molecules, typically proteins (Bhowmik et al., 2023). The current study aims to assess the potential of repellent compounds from the plants H. suaveolens and P. ampoinicus in blocking the odorant binding proteins of dengue and chikungunya vectors (Ae. aegypti and Ae. albopictus). Additionally, the study aims to understand their significant role in influencing the host-seeking and feeding behaviors of mosquitoes using in silico approaches.
In rational drug design, the initial step involves obtaining the structure of the target protein and the ligand molecule. Databases like PDB and PubChem provide access to a vast repository of compounds and proteins, numbering in the millions (Kim et al., 2019, 2021; Trudeau et al., 2023). A set of analytical techniques is applied with computer-assisted tools to identify compounds that exhibit the most favorable interactions with the protein target and thus merit consideration for drug synthesis.
Because there were no available three-dimensional structures for the Odorant Binding Protein (OBP) of Ae. albopictus, the structure was obtained from the AlphaFold database. The three-dimensional structures of the Odorant Binding Proteins from Ae. aegypti (PDB ID: 3K1E) and Ae. albopictus are depicted in Fig. 1.
The three-dimensional SDF structures of the processed ligands from the plants H. suaveolens and P. ampoinicus were obtained from the PubChem database (see Table 1) and prepared for docking with the mosquito odorant binding proteins. The calculations were carried out using Glide, a Schrodinger tool that conducts grid-based ligand docking with energetic considerations, seeking favorable interactions between small ligand molecules and a typical receptor molecule, usually a protein (Saini et al., 2023). Molecular docking was executed with the protein kept rigid, allowing the ligand to find its most suitable conformation.
Molecular docking analysis of Ae. aegypti OBP with compounds of H. suaveolens and P. ampoinicus
The simplest way to assess the accuracy of a docking procedure is to determine how closely it predicts the lowest energy pose, which represents the binding conformation. Three main parameters are considered in evaluating the results: G-score, hydrogen bond energy, and residual interaction. These parameters are used to discuss the binding affinity of the ligand towards the odorant binding receptor. A more negative G-score indicates a strong binding affinity between the ligand and the odorant binding receptor. A higher number of hydrogen bonds in the structure suggests that the ligand has a favorable binding mode with the receptor. The residual interaction provides information about the specific amino acid of the protein to which the ligand binds (Wang et al., 2023).
The results of molecular docking, as indicated by the G-score, hydrogen bonding, and interaction with residues, demonstrate the binding affinity of the ligands to the odorant binding protein. Specifically, chosen phytochemical compounds were used in the docking studies, and all these compounds successfully formed bonds with the Ae. aegypti odorant binding protein. The glide score, distance of hydrogen bonds, and the specific residues involved are presented in Table 2.
Table 2
Molecular docking of Aedes aegypti odorant binding protein (OBP) with different compounds from Hyptis suaveolens and Plectranthus ampoinicus
S. No.
|
Plant source
|
Compound Name
|
Dock Score
(kcal/mol)
|
Interacting Residues
|
Bond Length
(Å)
|
1.
|
H. suaveolens
|
N-dibenzofuran-3-yloxolane-2-carboxamide
|
-10.4
|
Ala88, His111, Trp114(3)
|
1.85, 5.25, 3.61, 4.16, 4.13
|
2.
|
H. suaveolens
|
Carvacryl acetate
|
-8.9
|
His111, Phe123
|
5.36, 1.94
|
3.
|
H. suaveolens
|
Brallobarbital
|
-8.4
|
Phe123
|
1.98
|
4.
|
H. suaveolens
|
2-Ethylacridine
|
-8.1
|
His111(2), Phe123(2)
|
4.93, 5.35, 2.32, 4.35
|
5.
|
H. suaveolens
|
Benzoic acid, 4-methyl-, hydrazide
|
-5.9
|
His111, Phe123
|
4.82, 2.08
|
6.
|
H. suaveolens
|
Aziridine, 1-(2-buten-1-yl), (E)-
|
-5.1
|
Phe123(2)
|
1.85, 4.35
|
7.
|
P. ampoinicus
|
3-Methyl-4-isopropylphenol
|
-7.5
|
His111, Phe123
|
5.48, 1.82
|
8.
|
P. ampoinicus
|
Thymol
|
-7.1
|
Phe123
|
2.00
|
Compound Tetrahydrofuran-2-carboxylic acid exhibited a good docking score − 10.4 (Kcal/mol) and formed a 5 H – bond with target OBP, and the amino acid residue was observed to be ALA 88, HIS 111 and TRP 114. The distance was recorded to be as 1.85Å, 5.25Å, 3.61Å, 4.16Å and 4.13Å respectively. The compound Carvacryl acetate, when docked with Ae. aegypti odorant binding protein recorded a docking score of −8.94 (Kcal/mol) and formed a 2 H – bond with target OBP, and the amino acid residue was observed to be HIS 111 and PHE123. The distance was recorded to be as 5.36 Å and 1.94 Å. The diagrammatic representation of the ligands Tetrahydrofuran-2-carboxylic acid, dibenzofuran-3-ylamide, Carvacryl acetate and Brallobarbital docked against Ae. aegypti OBP is represented in Figs. 2–4.
These results suggest that N-dibenzofuran-3-yloxolane-2-carboxamide, Carvacryl acetate and Brallobarbital exhibited a notable strong binding affinity and interaction with the Ae. aegypti Odorant Binding Protein (OBP). This suggests their potential to inhibit the mosquitoes' tendency to seek out humans, ultimately reducing contact between humans and the vector.
Molecular docking analysis of Ae. albopictus OBP with the compounds of H. suaveolens and P. ampoinicus
Compound Tetrahydrofuran-2-carboxylic acid and 3-Methyl-4-isopropylphenol exhibited good dock score (-7. 88 (Kcal/mol and − 6.9 (Kcal/mol)), and the number of H bonds were 5 and 1. The interactive residues of OBP with Tetrahydrofuran-2-carboxylic acid, dibenzofuran-3-ylamide are TRP148 and TYR390. The interactive residues of OBP with 3-Methyl-4-isopropylphenol is SER 144. The interaction of the ligand N-dibenzofuran-3-yloxolane-2-carboxamide and 3-Methyl-4-isopropylphenol docked against Ae. albopictus OBP is depicted in Figs. 5 and 6.
The results of molecular docking studies are displayed in Table 3. Similarly, OBP structures have been employed in homology modeling and molecular docking screening investigations to identify active semiochemicals in various insect pests. These pests include the oriental fruit fly (Bactrocera dorsalis) (Kamala Jayanthi et al., 2014), the Chilean scarab beetle (Hylamorpha elegans) (González-González et al., 2016), codling moth (Cydia pomonella) (Liu et al., 2016a), the leaf beetle (Ambrostoma quadriimpressum) (Wang et al., 2017), the polyphagous mirid bug (Adelphocoris lineolatus) (Sun et al., 2017), and the jujube bud weevil (Pachyrhinus yasumatsui) (Hong et al., 2022). Likewise, The larvicidal potential of the essential oil derived from H. suaveolens was examined, determining that the essential oil exhibits significant efficacy as a larvicide against Ae. aegypti (Moola et al. 2023).
Table 3
Molecular docking of Aedes albopictus odorant binding protein (OBP) with different compounds from Hyptis suaveolens and Plectranthus ampoinicus
S. No.
|
Plant Source
|
Compound Name
|
Dock Score
(kcal/mol)
|
Interacting Residues
|
Bond Length
(Å)
|
1.
|
H. suaveolens
|
N-dibenzofuran-3-yloxolane-2-carboxamide
|
-7.8
|
Trp148(3), Tyr390(2)
|
3.92, 4.15, 3.89, 2.15, 5.08
|
2.
|
H. suaveolens
|
2-Ethylacridine
|
-6.5
|
Trp148(5), Tyr390(2)
|
4.27, 4.32, 3.58,4.34, 4.35, 5.25, 4.68
|
3.
|
H. suaveolens
|
6-Chloro-3-ethyl-2-methyl-4-phenylquinoline
|
-5.6
|
Trp148, Lys180, Tyr390
|
3.58, 6.47, 5.37
|
4.
|
H. suaveolens
|
Carvacryl acetate
|
-5.3
|
Trp148(2), Tyr390
|
3.43, 4.23, 5.34
|
5.
|
H. suaveolens
|
4-methylbenzohydrazide
|
-5.2
|
Ser144, Trp148, Tyr390
|
2.06, 4.26, 4.74
|
6.
|
H. suaveolens
|
Brallobarbital
|
-4.9
|
Lys180
|
1.85
|
7.
|
H. suaveolens
|
1-[(E)-but-2-enyl] aziridine
|
-3.5
|
Trp148(2), Tyr390
|
4.68, 4.70, 4.47
|
8.
|
H. suaveolens
|
N-Methyl-1-adamantaneacetamide
|
-3.1
|
Leu177
|
1.77
|
9.
|
H. suaveolens
|
Cyclopentadecanone Oxime
|
-3.0
|
Pro178
|
2.31
|
10.
|
P. ampoinicus
|
3-Methyl-4-isopropylphenol
|
-6.9
|
Ser144
|
1.66
|
11.
|
P. ampoinicus
|
Thymol
|
-6.8
|
Ser144, Tyr390
|
1.83, 5.08
|
The compounds from H. suaveolens and P. ampoinicus demonstrated promising potential as natural mosquito repellents and offered a harmless alternative to conventional chemical pesticides. Molecular docking analyses reveal their strong interaction with OBP in Ae. aegypti and Ae. albopictus, crucial vectors of dengue and chikungunya. Tetrahydrofuran-2-carboxylic acid and Carvacryl acetate exhibit particularly high binding affinity with Ae. aegypti, while Tetrahydrofuran-2-carboxylic acid and 3-Methyl-4-isopropylphenol show significant interaction with Ae. albopictus OBP, highlighting their potential to disrupt mosquito attraction to humans.