Call for Paper - January 2024 Edition
IJCA solicits original research papers for the January 2024 Edition. Last date of manuscript submission is December 20, 2023. Read More

Virtual Screening and in vitro Assay to Explore Novel Inhibitors from Black Pepper against Potential Targets of Radopholus similis

International Journal of Computer Applications
© 2014 by IJCA Journal
Volume 86 - Number 14
Year of Publication: 2014
Rosana O. Babu
Krishna P. B.
Santhosh J. Eapen

Rosana O Babu, Krishna P B. and Santhosh J Eapen. Article: Virtual Screening and in vitro Assay to Explore Novel Inhibitors from Black Pepper against Potential Targets of Radopholus similis. International Journal of Computer Applications 86(14):35-43, January 2014. Full text available. BibTeX

	author = {Rosana O. Babu and Krishna P. B. and Santhosh J. Eapen},
	title = {Article: Virtual Screening and in vitro Assay to Explore Novel Inhibitors from Black Pepper against Potential Targets of Radopholus similis},
	journal = {International Journal of Computer Applications},
	year = {2014},
	volume = {86},
	number = {14},
	pages = {35-43},
	month = {January},
	note = {Full text available}


Radopholus similis, a migratory endoparasitic nematode that cause massive necrosis of plant tissues and destruction in host plants. The search for new nematode control molecules, particularly those of natural origin are of great urgency and importance. Phenylpropanoids belong to a major group of secondary metabolites produced by plants, mainly in defense response to biotic or abiotic stresses; literatures shows that chemical constituents of this family have bioactive compounds that can substitute current synthetic nematicides. But its efficacy and mode of action have not been demonstrated scientifically. In the present study, compounds from metabolic pathways of phenylpropanoid biosynthesis in black pepper (Piper nigrum L. ) have been screened for nematicidal and potential target inhibiting activity towards burrowing nematode, R. similis and the mechanism of inhibition of novel targets has been studied with molecular docking. The 3D structures of phenylpropanoid biosynthesis related phytochemicals were used as ligands. Available eight novel target protein (?-1, 4, endoglucanase, calreticulin-1, xylanase, cathepsin B-like cysteine proteinase, cathepsin S-like cysteine proteinase, cytochrome c-oxidase subunit III, glutathione S-transferase and transthyretin-like protein 3 precursor) of nematode associated with parasitic lifestyles and survival were selected as target molecule. Potential binding sites on each protein surfaces were predicted and screened phenylpropanoids have been docked to modeled targets of R. similis to assess their molecular interaction, binding energy and consequently their inhibitory activity. The docking results showed that thirteen phenylpropanoids possess similar dock score and hydrogen bond interactions, compared to current inhibitors and nematicides. Screening of these compounds in an in vitro assay showed that eight among the thirteen phenylpropanoids (syringaldehyde, salicylic acid, catechol, ferulic acid, coumaric acid, caffeic acid, tannic acid and N-vanillylnonanamide) caused maximum mortality to R. similis at 200ppm. Ferulic acid at 250ppm and 500ppm reduced R. similis population in infected black pepper in green house study. Hence the compounds represent promising starting points as lead compounds of natural origin that inhibit R. simlis; this provides possibility to further exploit these compounds in nematode management. The study also helps in understanding various aspects of phenylpropanoid pathways that can be manipulated for in-situ production and enhancement of these compounds.


  • Zunke U. (1991). Observations on the invasion and endoparasitic behaviour of the root lesion nematode Pratylenchus penetrans. J. Nematol. 22:309-320.
  • Brooks F. E. (2008). Burrowing Nematode. The Plant Health Instructor. DOI: 10. 1094/PHI-I-2008-1020-01.
  • Holdeman Q. L. (1986). The Burrowing Nematode Radopholus similis sensu lato. Nematology Publication, California Department of Food and Agriculture, Division of Plant Industry, Sacramento, CA, USA.
  • O'Bannon J. H. (1977). Worldwide dissemination of Radopholus similis and its importance in crop production. J. Nematol. 9(1):16-25.
  • Chitwood D. J. (2002). phytochemical based strategies for nematode control. Annu. Rev. Phytopathol. 40:221–49.
  • Gupta S. Bhandari Y. P. , Reddy M. V. , Harinath B. C. , Rathaur S. (2005). Setaria cervi: immunoprophylactic potential of glutathione-S-transferase against filarial parasite Brugia malayi. Exp Parasitol 109:252–255.
  • D. J. Pree, J. L. Townshend, and D. E. Archibald (1989). carbamate and organophosphorus nematicides: acetylcholinesterase inhibition and effects on dispersal. Journal of nematology 21(4):483-489.
  • Rosso M. N. , Jones J. T. , Abad P. (2009). RNAi and functional genomics in plant parasitic nematodes: tools and discoveries in the post-genomic era. Ann. Rev. Phytopathol 47:207-232.
  • Wuyts N. , Swennen R. , De Waele D. (2006). Effects of plant phenylpropanoid pathway products and selected terpenoids and alkaloids on the behaviour of the plant-parasitic nematodes Radopholus similis, Pratylenchus penetrans and Meloidogyne incognita. Nematology, 8(1,) 89-101(13).
  • Noling J. W. (2011). Movement and Toxicity of nematicides in the Plant Root Zone. ENY-041 (formerly RF-NG002), one of a series from the Department of Entomology and Nematology, Florida Cooperative Extension Service, Institute of Food and Agricultural Sciences, University of Florida.
  • Chitwood D. J. (2003). "Nematicides," in Encyclopedia of Agrochemicals (3), pp. 1104–1115, John Wiley & Sons, New York.
  • Collingborn F. M. B. , Gowen S. R. and Mueller-Harvey I. (2000). Investigations into the biochemical basis for nematode resistance in roots of three Musa cultivars in response to Radopholus similis infection. J. Agric. Food Chemistry 48: 5297-5301.
  • Dixon R. A. and Paiva N. L. (1995). Stress-induced phenylpropanoid metabolism. Plant Cell 7: 1085- 1097.
  • Douglas C. J. (1996). Phenylpropanoid metabolism and lignin biosynthesis: from weeds to trees. Trends Plant Sci. 1: 171-178.
  • Valette C. , Andary C. , Geiger J. P. , Sarah J. L. and Nicole M. (1998). Histochemical and cytochemical investigations of phenols in roots of banana infected by the burrowing nematode Radopholus similis. Phytopathology 88: 1141-1148.
  • Hahlbrock K. and Scheel D. (1989). Physiological and molecular biology of phenylpropanoid metabolism. Annu. Rev. Plant Physiol. Plant MoI. Biol. 40: 347-369.
  • Nicholson R. L. (1992). Phenolic compounds and their role in disease resistance. Annu. Rev. Phytopathol. 30: 369-389.
  • Jensen S. , Hansen J. and Boll P. M. (1993). Lignans and neolignans from Piperaceae. Phytochemistry 33: 523-530.
  • Parmar V. S. , Jain S. C. , Bisht K. S. , Jain R. , Taneja P. , Jha A. , Tyagi O. M. , Prasad A. K. , Wengel J. , Olsen, C. E. and Boll P. M. (1997). Phytochemistry of genus Piper. Phytochemistry 46: 597-673.
  • Korkina L. G. (2007). Phenylpropanoids as naturally occurring antioxidants: from plant defense to human health. Cell Mol. Biol. (Noisy-le-grand). 53 (1):15-25.
  • Masuda T. , Inazumi A. , Yamada Y. , Padolina W. G. , Kikuzaki H. and Nakatani N. (1991). Antimicrobial phenylpropanoids from Piper sarmentosum. Phytochemistry 30: 3227-3228.
  • Eswar N. , Marti-Renom M. A. , Webb B. , Madhusudhan M. S. , Eramian D. , Shen M. , Pieper U. , Sali A. (2006). Comparative Protein Structure Modeling With MODELLER. Current Protocols in Bioinformatics, John Wiley & Sons, Inc. , Supplement 15, 5. 6. 1-5. 6. 30.
  • Yang Z. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9:40.
  • Marchler-Bauer A, Zheng C, Chitsaz F, Derbyshire MK, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Lu S, Marchler GH, Song JS, Thanki N, Yamashita RA, Zhang D, Bryant SH. (2013. ) CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res. Jan 1;41(D1):D348-52.
  • Laskowski R A. (2001). PDBsum: summaries and analyses of PDB structures. Nucleic Acids Res. , 29, 221-222.
  • Rob W. W. Hooft, Chris Sander and Gerrit Vrien (1997). Objectively judging the quality of a protein structure from a Ramachandran plot. Comput. Appl Biosci. 13: 425
  • Eisenberg D. , Luthy R. , Bowie JU. (1997). VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol. 277:396-404
  • Colovos C. and Yeates T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Sci. 2:1511–1519.
  • Peng, C. , Ayali, P. Y. , Schlegel, H. B. and Frisch M. J. (1995). Using redundant internal coordinates to optimize equilibrium geometries and transition states. J. Comput. Chem. 16: 49–51.
  • Filimonov D. A. and Poroikov V. V. (1996). PASS: Computerized prediction of biological activity spectra for chemical substances. Bioactive Compound Design. Possibilities for Industrial Use. BIOS Scientific, Oxford, pp. 47–56.
  • Thomsen R. and Christensen M. H. (2006). MolDock: a new technique for high-accuracy molecular docking. J. Med. Chem. 49: 3315–3321.
  • Korb O. , Stutzle T. and Exner T. E. (2009). Empirical scoring functions for advanced protein-ligand docking with PLANTS. J. Chem. Inf. Model. 49: 84–96.
  • Yang JM and Chen CC. (2004). GEMDOCK: a generic evolutionary method for molecular docking. Proteins: 55(2):288-304.
  • Meher H. C. , Gajbhiya V. T. , Singh G. , Kamara A. & Chawla G. (2010). Persistence and nematicidal efficacy of carbofuran, cadusa fos, phorate and triazophos in soil and uptake by chickpea and tomato crops under tropical conditions. J. Agric. Food Chem. , 58: 1815-1822.
  • Michalak M, Milner RE, Burns K, Opas M. (1992). Calreticulin. Biochem J. 1992 Aug 1;285 ( Pt 3):681- 92.
  • Sheridan J. p. , Miller A. J. and Perry R. N. (2004). Early responses of resistant and susceptible potato roots during invasion by the potato cyst nematode Globodera rostochiensis, Journal of Experimental Botany 55, 751-760.
  • Abad P, Favery B, Rosso MN, Castagnone-Sereno P. (2003). Root-knot nematode parasitism and host response: molecular basis of a sophisticated interaction. Molecular Plant Pathology 4, 217-224.
  • Shibuya H. and Kikuchi T. (2008). Purification and characterization of recombinant endoglucanases from the pine wood nematode Bursaphelenchus xylophilus. Biosci. Biotechnol. Biochem. 72 (5): 1325–1332.
  • Haegeman A. , Jacob J. , Vanholme B. , Kyndt T. and Gheysen G. , (2008). A family of GHF5 endo-1,4-beta-glucanases in the migratory plant-parasitic nematode Radopholus similis. Plant Pathol. 57, 581-590.
  • Goellner M. , Wang X. , and Davis E. L. (2001). Endo-b-1,4-glucanase expression in compatible plant-nematode interactions. The Plant Cell 13:2241–2255.
  • Wang X. , Meyers D. , Yan Y. , Baum T. , Smant G. , Hussey R. , and Davis E. (1999). In planta localization of a b-1,4-endoglucanase secreted by Heterodera glycines. Molecular Plant-Microbe Interactions 12:64–67.
  • Bakhetia M. , Urwin P. E. , and Atkinson H. J. (2007). qPCR analysis and RNAi define pharyngeal gland cell-expressed genes of Heterodera glycines required for initial interactions with the host. Molecular Plant- Microbe Interactions 20:306–312.
  • Chen Q. , Rehman S. , Smant G. , and Jones J. T. (2005). Functional analysis of pathogenicity proteins of the potato cyst nematode Globodera rostochiensis using RNAi. Molecular Plant-Microbe Interactions 18:621–625.
  • Rehman S. , Butterbach P. , Popeijus H. , Overmars H. , Davis E. L. , Jones J. T. , Goverse A. , Bakker J. , and Smant G. (2009). Identification and characterization of the most abundant cellulases in stylet secretions from Globodera rostochiensis. Phytopathology 99:194–202.
  • Makedonka Mitreva-Dautova, Erwin Roze, Hein Overmars, Leo de Graaff, Arjen Schots, Johannes Helder, Aska Goverse, Jaap Bakker, and Geert Smant (2006. ) A Symbiont-Independent Endo-1,4- ?-Xylanase from the Plant-Parasitic Nematode Meloidogyne incognita. MPMI Vol. 19, No. 5, pp. 521–529.
  • Banik M. , Garrett T. P. J. , and Fincher G. B. (1996). Molecular cloning of cDNAs encoding (1-4)-beta-xylan endohydrolases from the aleurone layer of germinated barley (Hordeum vulgare). Plant Mol. Biol. 31:1163-1172.
  • Bih F. Y. , Wu S. S. H. , Ratnayake C. , Walling L. L. , Nothnagel E. A. , and Huang A. H. C. (1999). The predominant protein on the surface of maize pollen is an endoxylanase synthesized by a tapetum mRNA with a long 5? leader. J. Biol. Chem. 274:22884-22894.
  • Chen N. J. , and Paull R. E. (2003). Endoxylanase expressed during papaya fruit ripening: Purification, cloning and characterization. Funct. Plant Biol. 30:433-441.
  • Suzuki M. , Kato A. , Nagata N. , and Komeda Y. (2002). A xylanase, AtXyn1, is predominantly expressed in vascular bundles, and four putative xylanase genes were identified in the Arabidopsis thaliana genome. Plant Cell Physiol. 43:759-767.
  • Guiliano DB, Hong X, McKerrow JH, Blaxter ML, Oksov Y, et al. (2004). A gene family of cathepsin L-like proteases of filarial nematodes are associated with larval molting and cuticle and eggshell remodeling. Mol Biochem Parasitol 136(2): 227–242.
  • Sankale Shompole and Douglas P. Jasmer (2001). Cathepsin B-like Cysteine Proteases Confer Intestinal Cysteine Protease Activity in Haemonchus contort. Vol. 276, No. 4, Issue of January 26, pp. 2928–2934.
  • Urwin P. E. , Lilley C. J. , McPherson M. J. , Atkinson H. J. (1997). Characterization of two cDNAs encoding cysteine proteinases from the soybean cyst nematode Heterodera glycines. Parasitology 114:605-613.
  • Calhoun M. W. , Thomas J. W. , Gennis R. B. (1994). The cytochrome oxidase superfamily of redox-driven proton pumps. Trends Biochem. Sci, 19, pp. 325–330 95026991.
  • Jacob JE. (2009). A unique genetic code change in the mitochondrial genome of the parasitic nematode Radopholus similis. BMC Res Notes, 2009 Sep 24. PMID 19778425.
  • Brophy P. M. and Barrett J (1990). Glutathione-S-transferase in helminths. Parasitology 100: 345–349.
  • Brophy P. M. and Pritchard D. I. (1992). Immunity to helminths: ready to tip the biochemical balance. Parasitol. Today 8: 419–422.
  • Ahmad R. , Srivastava A. K. and Walter R. D. (2008a). Puri?cation and biochemical characterization of cytosolic glutathione-S-transferase from ?larial worms Setaria cervi. Comparative Biochemistry and Physiology, Part B 151: 237–245.
  • Bhargavi R, Vishwakarma S, Murty US (2005). Modeling analysis of GST (glutathione-S-transferases) from Wuchereria bancrofti and Brugia malayi. Bioinform 1:25–27.
  • Jacob J, Vanholme B, Haegeman A, Gheysen G (2007). Four transthyretin-like genes of the migratory plant-parasitic nematode Radopholus similis: members of an extensive nematode-specific family. Gene. Nov 1; 402(1-2):9-19
  • McCarter JP, Mitreva MD, Martin J, Dante M, Wylie T, et al. (2003). Analysis and functional classification of transcripts from the nematode Meloidogyne incognita. Genome Biology 4(4): R26.
  • Palha JA (2002). Transthyretin as a thyroid hormone carrier: Function revisited. Clin Chem Lab Med 40: 1292-1300.