Studies on Interaction of Insect Repellent Compounds with Odorant Binding Receptor Proteins by in silico Molecular Docking Approach

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1 Interdiscip Sci Comput Life Sci (2013) 5: DI: /s Studies on Interaction of Insect Repellent Compounds with dorant Binding Receptor Proteins by in silico Molecular Docking Approach J. Vinay GPAL, K. KANNABIRAN (Division of Biomolecules and Genetics, School of Biosciences and Technology, VIT University, Vellore , India) Received 14 August 2012 / Revised 27 November 2012 / Accepted 21 January 2013 Abstract: The aim of the study was to identify the interactions between insect repellent compounds and target olfactory proteins. Four compounds, camphor (C 10H 16), carvacrol (C 10H 14), oleic acid (C 18H 34 2)and firmotox (C 22H 28 5) were chosen as ligands. Seven olfactory proteins of insects with PDB IDs: 3K1E, 1QWV, 1TUJ, 1F, 2ERB, 3R1 and BP1 were chosen for docking analysis. Patch dock was used and pymol for visualizing the structures. The interactions of these ligands with few odorant binding proteins showed binding energies. The ligand camphor had showed a binding energy of 136 kcal/mol with BP1 protein. The ligand carvacrol interacted with 1QWV and 1TUJ proteins with a least binding energy of kcal/mol and kcal/mol respectively. The ligand oleic acid interacted with 1F, 2ERB, 3R1 and BP1 with least binding energies. Ligand firmotox interacted with BP1 and showed least binding energies. Three ligands (camphor, oleic acid and firmotox) had one, two, three interactions with a single protein BP1 of Nilaparvatha lugens (Rice pest). From this in silico study we identified the interaction patterns for insect repellent compounds with the target insect odarant proteins. The results of our study revealed that the chosen ligands showed hydrogen bond interactions with the target olfactory receptor proteins. Key words: patch dock, pymol, insect repellent compounds, odarant binding proteins. 1 Introduction Repellents are substances that deter insects from biting and landing on human or animal skin surface (Blackwell et al., 2003). The use of synthetic repellents has increased worldwide especially to prevent spoilage of fruits, grains and to control vector-borne diseases like malaria, dengue and yellow fever (Nerio et al., 2009). Synthetic repellents used to control insects may have severe effects on environment and human health (Pitasawat et al., 2003). Thus there is a tendency to increase the usage of natural and environment friendly repellents due to their low toxicity and safety (Katz et al., 2008). In the last 50 years many plants have been screened for novel repellents and insecticide activities (Sukumar et al., 1991). The major proteins of the insect olfactory system are the odarant binding proteins (BPs) (Vogt et al., 1981). Insect BPs are of three types, pheromone binding proteins (PBPs), general odarant binding proteins and antennal binding proteins (AB- PXs) (Zhou et al., 2010). These BPs are small soluble proteins that help in transport of signals from odarant compounds to brain that mediate insect behavioural response (Xu et al., 2010). Corresponding author. kkb@vit.ac.in In silico and computational simulation methods are useful for making logistic predictions and hypothesizing to find out solutions in the areas of medicine and drug formulation. The use of natural products with insect repellent property can be identified by using in silico molecular docking tools. These methods provide suitable insights into identifying binding residues responsible for a biological function. In this study we performed docking of certain natural repellent compounds with olfactory proteins of insects to understand their binding patterns. 2 Materials and methods 2.1 Ligands The ligand molecules selected for this study were camphor (C 10 H 16 ), carvacrol (C 10 H 14 ), oleic acid (C 18 H 34 2 ) and firmotox (C 22 H 28 5 ). The 3D conformations of the compounds were obtained from NCBI database by copying the canonical smiles in CRINA software (Fig. 1) Target proteins A total of 7 proteins were selected as targets for docking which include odorant binding proteins with PDB

2 Interdiscip Sci Comput Life Sci (2013) 5: H (a) H (b) Fig. 1 (c) (d) Chemical structures. (a) Camphor; (b) Carvacrol; (c) leic acid; (d) Firmotox. IDs: 3K1E, 1QWV, 1TUJ, 1F, 2ERB, 3R1 and a modelled protein BP1 of Nilaparvatha lugens using i-tasser ( TASSER/). 2.3 Molecular docking studies Molecular docking was carried out using patch dock online tool. The input file was in the form of PDB code of the receptor or pdb file format and the molecules were in pdb file format. The output file was as a docking report. The docked image was viewed by Pymol 1.3 software. The interactions between ligands and proteins were also seen with the length of the interaction along with amino acids involved in these interactions and it was calculated by using Pymol 1.3 software. The binding energy was calculated by Atomic contact energy (ACE) according to Zhang et al. (1997). 3 Results and discussion The four different natural repellent compounds were docked with seven odarant receptor proteins (Fig. 2). C 10 H 16 3K1E BP1 C 10 H 14 1QWV 1TUJ C 18 H F 2ERB 3R1 BP1 Fig. 2 C 22 H 28 5 BP1 In silico molecular docking analysis of four target compounds against seven odarant binding proteins (BPs).

3 282 Interdiscip Sci Comput Life Sci (2013) 5: ut of the four ligands the first compound camphor (IUPAC name: 4, 7, 7-trimethylbicyclo [2.2.1] heptan- 3-one), possesses 16 non polar hydrogens. The docking of camphor with seven odorant binding proteins resulted with two interactions between the ligand and receptor proteins 3K1E and BP1. Camphor showed aminoacid interactions with 3K1E protein from Aedes aegyptii with a least binding energy of 4.14 kcal/mol and BP1 modelled protein of Nilaparvatha lugens (rice pest pathogen) with a least binding energy of kcal/mol. ne interaction was observed between camphor and 3K1E protein (Table 1). Table 1 Docking results of insect repellent compounds against olfactory receptor proteins Ligand Target proteins Score Area ACE (kcal/m) Hydrogen bond Camphor 3K1E (Aedes aegypti) (C 10 H 16 ) BP1 (Nilaparvatha lugens) Carvacrol 1QWV (Antheraea Polyphemus) (C 10 H 14 ) 1TUJ (Apis mellifera) leic acid 1F (Drosophila melanogaster) (C 18 H 34 2 ) 2ERB (Anopheles gambiae) R1 (Anopheles gambiae) BP1 (Nilaparvatha lugens) Firmotox BP1 (Nilaparvatha lugens) (C 22 H 28 5 ) The length of the interaction between the ligand and the target protein was 3.0 Å. Lysine is situated at 112 th position in the amino acid sequence of 3K1E protein and it has 9 atoms (Fig. 3). PHE LYS Fig. 4 In silico binding of camphor with BP1 from Nilaparvatha lugens. Fig. 3 In silico binding of camphor with 3K1E protein. A single interaction was observed between amino acid phenylalanine and camphor (ligand). The length of the interaction was calculated as 3.3 Å. Phenylalanine was located at 169 th position in the amino acid sequence of i TASSER modelled protein BP1 from Nilaparvatha lugens and it has 11 atoms (Fig. 4). The second compound carvacrol (IUPAC name: 2- methyl-5-propan-2-ylphenol), has 13 non polar hydrogens, 6 aromatic carbons and 2 rotatable bonds. The ligand showed interactions with pheromone binding protein (PDB ID: 1QWV from Antheraea polyphemus) and odorant binding protein (1TUJ from Apis mellifera) with least binding energies of and kcal/mol respectively. Isoleucine at 52 nd position had interaction with 1QWV protein with bond length of 2.0 Å and contains 19 atoms (Fig. 5). Carvacrol interacted with serine at 123 rd position of 1TUJ, an odorant bind-

4 Interdiscip Sci Comput Life Sci (2013) 5: ILE-52 GLN Fig. 5 In silico binding of carvacrol with 1QWV protein. Fig. 7 In silico binding of oleic acid with 1F protein. SER SF Fig. 8 In silico binding of oleic acid with 2ERB protein. Fig. 6 In silico binding of carvacrol with 1TUJ protein. ing protein from Apis mellifera with a bond length of 1.5 Å and has 11 atoms (Fig. 6). The third compound oleic acid (IUPAC name: (Z)- octadec-9-enoic acid), has 33 non polar hydrogens and 16 rotatable bonds. This ligand interacted with four proteins 1F, 2ERB, 3R1 and BP1 from Nilaparvatha lugens. The ligand interacted with glutamine residue (5 th position) from Drosophila melanogaster with nine atoms and a binding energy of kcal/mol and the length of interaction was 3.4 Å (Fig. 7). leic acid showed interaction with aspartic acid (at 67 th position) of 2ERB protein from Anopheles gambiae with a binding energy of kcal/mol and bond length of 2.9 Å, and it possesses 8 atoms (Fig. 8). The oleic acid interacted with odarant protein from Anopheles gambiae and two interactions with BP1 protein from Nilaparvatha lugens also occurred. Tyrosine at 74 th position showed binding with 3R1 protein with 24 atoms and bond length of 2.8 Å (Fig. 9). The ligand also interacted with BP1 protein with glutamine and lysine residues at 61 st and 64 th positions with a bond length of 2.1 Å and 2.9 Å respectively (Fig. 10). Firmotox (IUPAC Name: [2-methyl-4-oxo-3-[(2Z)- penta-2, 4-dienyl] cyclopent-2-en-1-yl](1r, 3R)-3-[(E)- 2-acetyloxyprop-1-enyl]-2, 2dimethylcyclo propane-1- carboxylate), has 28 non-polar hydrogens, 8 aromatic carbons and 9 rotatable bonds. The ligand interacted with BP1 protein from Nilaparvatha lugens. The

5 284 Interdiscip Sci Comput Life Sci (2013) 5: TYR-74 LYS Fig. 9 In silico binding of oleic acid with 3R1. Fig. 11 In silico binding of firmotox with BP1 from Nilaparvatha lugens. odours, BP1 protein was reported to show high binding affinity to camphor and some structurally related compounds. Fig. 10 GLU LYS-64 In silico binding of oleic acid with BP1 from Nilaparvatha lugens. amino acids involved were lysine at 64 th position with 9atoms,75 th position containing 9 atoms and serine at 71 st position with 6 atoms. The bond lengths for lysine at 64 th and 75 th positions were 3.0 Åand1.8Å respectively, and the bond length of serine at 71 st position was 3.4 Å (Fig. 11). Structure based modelling predictions may facilitate the design of novel repellents with increased binding affinity and selectivity (Tsitsanou et al., 2012). Some monoterpenes such as camphor and carvacrol are constituents of essential oils and were reported to have mosquito repellent activity (Ibrahim et al., 1998; Jaenson et al., 2006; Park et al., 2005; Yang et al., 2004). Insect odarant binding proteins are components of olfactory system that binds to attractant and repellent 4 Conclusions We concluded that the hydrogen bond interactions occurred involving the amino acid residues of the target odarant receptor proteins (PDB IDs: 3K1E, 1QWV, 1TUJ, 2ERB, 1F, 3R1 and BP1) of Nilaparvath a with selected ligands (camphor, carvacrol, oleic acid and firmotox) which are often used for insecticidal repellent activity. These results further substantiate the use of in silico tools for identifying novel insect repellent compounds. Acknowledgements Authors thank the management of VIT University for providing necessary facilities to carry out this study. References [1] Blackwell, A., Stuart, A.E., Estambale, B.A The repellent and antifeedant activity of oil of Myrica gale against Aedes aegypti mosquitoes and its enhancement by the addition of salicyluric acid. JR Coll Physicians Edinb 33, [2] Ibrahim, J., Zaki, Z.M Development of environment-friendly insect repellents from the leaf oils of selected Malaysian Plants. ASEA Rev Biodiv Environ Conserv (ARBEC) 6, 1-7. [3] Jaenson, T.G., Palsson, K., Borg-Karlson, A.K Evaluation of extracts and oils of mosquito (Diptera: Culicidae) repellent plants from Sweden and Guinea- Bissau. J Med Entomol 43,

6 Interdiscip Sci Comput Life Sci (2013) 5: [4] Katz, T., Miller, J., Hebert, A Insect repellents: historical perspectives and new developments. J Am Acad Dermatol 58, [5] Nerio, L.S., livero-verbel, J., Stashenko, E Repellent activity of essential oils: A review. Bioresource Technol 101, [6] Park, B.S., Choi, W.S., Kim, J.H., Lee, S.E Monoterpenes from thyme (Thymus vulgaris) as potential mosquito repellents. J Am Mosq Contr Assoc 21, [7] Pitasawat, B., Choochote, W., Tuetun, B., Tippawangkosol, P., Kanjanapothi, D., Jitpakdi, A., Riyong, D Repellency of aromatic turmeric Curcuma aromatica under laboratory and field conditions. J Vector Ecol 28, [8] Sukumar, K., Perich, M.J., Boobar, L.R Botanical derivatives in mosquito control: A review. J Am Mosq Control Assoc 7, [9] Tsitsanou, K.E., Thireou, T., Drakou, C.E., Koussis, K., Keramioti, M.V., Leonidas, D.D., Eliopoulos, E., Iatrou, K., Zographos, S.E Anopheles gambiae odorant binding protein crystal complex with the synthetic repellent DEET: Implications for structurebased design of novel mosquito repellents. Cell Mol Life Sci 69, [10] Vogt, R.G., Riddiford, L.M Pheromone binding and inactivation by moth antennae. Nature 293, [11] Xu, W., Cornel, A.J., Leal, W.S dorantbinding proteins of the malaria mosquito anopheles funestus sensu strict. PLoS NE 5, e [12] Yang, Y.C., Lee, E.H., Lee, H.S., Lee, D.K., Ahn, Y.J Repellency of aromatic medicinal plant extracts and a steam distillate to Aedes aegypti. JAmMosq Contr Assoc 20, [13] Zhang, C., Vasmatzis, G., Cornette, J.L., Delisi, C Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol 267, [14] Zhou, J.J dorant-binding proteins in insects. Vitam Horm 83,