Identification of Potential Nematicidal Compounds against the Pine Wood Nematode, Bursaphelenchus xylophilus through an In Silico Approach
Abstract
1. Introduction
2. Results and Discussion
2.1. Target–Template Alignment for Homology Modeling
2.2. Homology Modeling
2.3. Model Validation
2.4. Structure-Based Virtual Screening
2.5. Density Functional Theory Analysis
3. Materials and Methods
3.1. Sequence Analysis for Potential Templates
3.2. Homology Modeling
3.3. Model Validation
3.4. Structure-Based Virtual Screening
3.5. Docking Interactions
3.6. Electronic Structure Study of Selected Screening Compounds
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Sample Availability: All the compounds are available from Pubchem and ZINC database. |
Sl. No. | Target | Function |
---|---|---|
1. | Cathepsin L-like cystein proteinase (BxCLCP) (UniProt ID: Q6LDJ1) | Post embryonic development |
2. | 2-cysteine peroxiredoxin (BxPRX) (UniProt ID: B0LFQ7) | Reproduction and pathogenecity |
3. | Heat Shock Protein 90 (BxHSP90) (UniProt ID: A4UU63) | Adapts to different climatic conditions |
4. | Venom allergen Protein-3 (BxVAP-3) (UniProt ID: E0WW94) | Invasion parasitic genes |
5. | β-Tubulin (BxTUB) (UniProt ID: D1MX18) | Microtubule, mitosis, motility |
Compound Name (Pubchem Id) | Cathepsin L-Like Cystein Proteinase (BxCLCP) | 2-Cysteine Peroxiredoxin (BxPRX) | Heat Shock Protein 90 (BxHSP90) | Venom Allergen Protein-3 (BxVAP-3) | β-Tubulin (BxTUB) |
---|---|---|---|---|---|
Kainic acid (CID 10255) | −17.653 | −18.586 | −11.942 | −12.681 | −24.909 |
Carbendazim (CID 25429) | −14.879 | −16.525 | −12.365 | −15.173 | −21.44 |
Naphthalen-2-ol (CID 8663) | −9.5734 | −11.793 | −9.6124 | −11.458 | −12.053 |
Pyrantel (CID 708857) | −8.0396 | −12.548 | −8.519 | −9.0794 | −12.559 |
Closantel (CID 42574) | −15.618 | −6.0856 | −8.3846 | −15.835 | −14.155 |
Thiabendazole (CID 5430) | −12.071 | −15.395 | −12.1 | −13.143 | −16.532 |
Schaftoside (CID 442658) | −10.435 | −9.6139 | −4.0356 | −5.3029 | −22.876 |
Mebendazole (CID 4030) | −18.322 | −20.111 | −18.993 | −18.699 | −25.531 |
Oxfendazole (CID 40854) | −15.653 | −19.8592 | −13.344 | −17.071 | −21.242 |
Levamisole (CID 26879) | −8.1927 | −12.361 | −6.1674 | −12.326 | −13.724 |
Tetramizole (CID 3913) | −6.7261 | −10.75 | −5.2535 | −12.811 | −17.188 |
Coumafos (CID 2871) | −6.7703 | −18.175 | −1.7963 | −5.8927 | −15.065 |
Amocarzine (CID 5464102) | −18.752 | −30.163 | −22.895 | −19.279 | −27.122 |
Fenbendazole (CID 3334) | −14.391 | −18.826 | −14.743 | −14.202 | −24.141 |
Flubendazole (CID 35802) | −19.364 | −23.2623 | −15.053 | −17.962 | −28.058 |
Potential Targets from B. xylophilus | Best Docked Compounds | ||
---|---|---|---|
Amocarzine (CID 5464102) | Flubendazole (CID 35802) | Mebendazole (CID 4030) | |
Cathepsin L-like cystein proteinase (BxCLCP) (UniProt ID: Q6LDJ1) | #Gln26 *, His27 #Glu28 *, Lys113 Thr206 * | Ile25 *, #Gln62 * #Cys65 *, Gly66 Cys68, Thr206 * His207, Trp230 | #Gln62 *, #Cys65 *, Gly66, #Trp230 * |
−18.752 | −19.364 | −18.322 | |
2-cysteine peroxiredoxin (BxPRX) (UniProt ID: B0LFQ7) | Ile6, Arg137 * Gln138, Ile139 * Leu156, Glu152 * Phe160 | Ile6, Arg137 * #Gln138 *, #Ile139 *, Phe160 | Ile6, Arg137 * Gln138, #Ile139 * Phe160 |
−30.163 | −23.2623 | −20.111 | |
Heat Shock Protein 90 (BxHSP90) (UniProt ID: A4UU63) | #Lys332 *, Ala333 Gln334, #Arg337 * Asp338, Ser339 Met342 | #Met331*, Lys332 #Gln334 *, Ala335, #Arg337 * | Met331 *, Lys332 Ala333, Gln334* Ala335, #Arg337 * |
−22.895 | −15.053 | −18.993 | |
Venom allergen Protein-3 (BxVAP-3) (UniProt ID: E0WW94) | #Trp95 *, #Pro96 * His97, #Asn160 * | Ala93, Gln94 #Trp95 *, #Asn160 *, Trp161 | Ala93, Gln94 #Trp95 *, #Asn160 * Trp161 |
−19.279 | −17.962 | −18.699 | |
β-Tubulin (BxTUB) (UniProt ID: D1MX18) | Gln11, Gly98 * #Asn99 *, Ser138 Gly141, Thr143 * Ser176, #Asp177 * Glu181, Asn204 | Gln11 *, Cys12 #Asn99 *, Gly141 Gly142 *, Thr143 * Asp177, Thr178 Asn204, Tyr222 | Gln11, #Cys12 * Ser138, Gly141 Val169, Ser172 * #Asp177 *, Asn204 * Tyr222 |
−27.122 | −28.058 | −25.531 |
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Shanmugam, G.; Lee, S.K.; Jeon, J. Identification of Potential Nematicidal Compounds against the Pine Wood Nematode, Bursaphelenchus xylophilus through an In Silico Approach. Molecules 2018, 23, 1828. https://doi.org/10.3390/molecules23071828
Shanmugam G, Lee SK, Jeon J. Identification of Potential Nematicidal Compounds against the Pine Wood Nematode, Bursaphelenchus xylophilus through an In Silico Approach. Molecules. 2018; 23(7):1828. https://doi.org/10.3390/molecules23071828
Chicago/Turabian StyleShanmugam, Gnanendra, Sun Keun Lee, and Junhyun Jeon. 2018. "Identification of Potential Nematicidal Compounds against the Pine Wood Nematode, Bursaphelenchus xylophilus through an In Silico Approach" Molecules 23, no. 7: 1828. https://doi.org/10.3390/molecules23071828
APA StyleShanmugam, G., Lee, S. K., & Jeon, J. (2018). Identification of Potential Nematicidal Compounds against the Pine Wood Nematode, Bursaphelenchus xylophilus through an In Silico Approach. Molecules, 23(7), 1828. https://doi.org/10.3390/molecules23071828