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Molecular Docking Study of CHS Gene from a Medicinally Important Orchid, Coelogyne ovalis Lindl.


Affiliations
1 Department of Botany, Plant Biotechnology Laboratory, North-Eastern Hill University, Shillong 793 022, India
 

Chalcone synthase (CHS) is an important enzyme belonging to the polyketide synthase (type III) family. It is well known for substrate specificity and catalyses diverse groups of polyketides of pharmaceutical value. In the present study, the structure of the CHS protein has been predicted from the medicinal orchid, Coelogyne ovalis Lindl. This is an evergreen orchid, well known for its medicinal uses. The homology-based model was constructed from CHS of C. ovalis (CoCHS) and 16 different ligands were used based on the specificity for molecular docking studies. The four best ligands on the basis of greater negative binding energy were found to be 3-carbomoyl-picoliniyl CoA, followed by carbomoyl-2-napthoyl CoA, p-coumaroyl CoA and malonyl CoA. The present structural study reveals that CoCHS has signature and catalytic amino acid residues, namely Cys165, Asn337, His 306, Phe216 and Phe 266. These residues are known to have a broad-range substrate profile and are responsible for the binding of protein ligands. The present study elucidates the chemical basis of CHS from C. ovalis by understanding the structural and functional relationship. This provides an insight for manipulating the enzymes, CHS-like for the synthesis of new bioactive compounds, which may further enhance the diversity of the polyketide biosynthetic family

Keywords

Coelogyne ovalis, Chalcone Synthase, Ligands, Molecular Docking, Polyketides.
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  • Koes, R. E., Spelt, C. E. and Mol, J. N., The chalcone synthase multigene family of Petunia hybrida: differential, light regulated expression during flower development and UV light induction. Plant Mol. Biol., 1989, 12, 213–225.

  • Vogt, T., Phenylpropanoid biosynthesis. Mol. Plant, 2010, 3, 2–20.

  • Tohge, T., Yonekura-Sakakibara, K., Niida, R., WantanabeTakahasi, A. and Saito, K., Phytochemical genomics in Arabidopsis thaliana: a case study for functional identification of flavonoid biosynthesis gene. Pure Appl. Chem., 2007, 79, 811–823.

  • Harborne, J. B. and Turner, B. L. (eds), Application of chemistry at the infraspecific level. In Plant Chemosystematics, Academic Press, London, UK, 1984, pp. 237–266.

  • Dixon, R. A., The phytoalexin response: elicitation, signalling and control of host gene expression. Biol. Rev., 1986, 61, 239–291.

  • Schmelzer, E., Jahnen, W. and Hahlbrock, K., In situ localization of light-induced chalcone synthase mRNA, chalcone synthase, and flavonoid end products in epidermal cells of parsley leaves. Proc. Natl. Acad. Sci. USA, 1988, 85, 2989–2993.

  • Abe, I., Takahashi, Y. and Noguchi, H., Enzymatic formation of an unnatural C6–C5 aromatic polyketide by plant type III polyketide synthases. Org. Lett., 2002, 4, 3623–3626.

  • Dao, T. T., Linthorst, H. J. and Verpoorte, R., Chalcone synthase and its functions in plant resistance. Phytochem. Rev., 2011, 10, 397–412.

  • Morita, H., Takahashi, Y., Noguchi, H. and Abe, I., Enzymatic formation of unnatural aromatic polyketides by chalcone synthase. Biochem. Biophys. Res. Commun., 2000, 279, 190–195.

  • Oguro, S., Akashi, T., Ayabe, S. I., Noguchi, H. and Abe, I., Probing biosynthesis of plant polyketides with synthetic N-acetylcysteamine thioesters. Biochem. Biophys. Res. Commun., 2004, 325, 561–567.

  • Reddy, A. R., Scheffler, B., Madhuri, G., Srivastava, M. N., Kumar, A., Sathyanarayanan, P. V. and Mohan, M., Chalcone synthase in rice (Oryza sativa L.): detection of the CHS protein in seedlings and molecular mapping of the CHS locus. Plant Mol. Biol., 1996, 32, 735–743.

  • Awasthi, P., Mahajan, V., Jamwal, V. L., Kapoor, N., Rasool, S., Bedi, Y. S. and Gandhi, S. G., Cloning and expression analysis of chalcone synthase gene from Coleus forskohlii. J. Genet., 2016, 95, 647–657.

  • Goodwin, P. H., Hsiang, T. and Erickson, L., A comparison of stilbene and chalcone synthases including a new stilbene synthase gene from Vitis riparia cv. Gloire de Montpellier. Plant Sci., 2000, 151, 1–8.

  • Yamazaki, Y. et al., Diverse chalcone synthase superfamily enzymes from the most primitive vascular plant, Psilotum nudum. Planta, 2001, 214, 75–84.

  • Jiang, C., Schommer, C. K., Kim, S. Y. and Suh, D. Y., Cloning and characterization of chalcone synthase from the moss, Physcomitrella patens. Phytochemistry, 2006, 67, 2531–2540.

  • Wang, M. X., Li, W. L., Zhang, Z., Wei, J. H., Yang, Y., Xu, Y. H. and Liang, L., Cloning and bioinformatics analysis of chalcone synthase (AsCHS1) gene in Aquilaria sinensis. China J. Chin. Mater. Med., 2013, 38, 149–153.

  • Singh, N. and Kumaria, S., Molecular cloning and characterization of chalcone synthase gene from Coelogyne ovalis Lindl. and its stress-dependent expression. Gene, 2007, 762, 145104.

  • Nongrum, I., Kumaria, S. and Tandon, P., Influence of in vitro media on asymbiotic germination, plantlet development and ex vitro establishment of Coelogyne ovalis and Coelogyne nitida. Proc. Indian Natl. Sci. Acad., 2007, 73, 205–207.

  • Yonzone, R., Lama, D., Bhujel, R. B. and Rai, S., Present availability status, diversity resources and distribution of medicinal orchid species in Darjeeling Himalaya of West Bengal, India. Int. J. Pharm. Nat. Med., 2013, 1, 14–35.

  • Majumder, P. L. and Laha, S., Occurrence of 2,7-dihydroxy-3,4-6trimethoxy-9,10-dihydropenanthrene in Coelogyne ovalis, a high altitude Himalayan orchid: application of C-13 NMR spectroscopy in structure elucidation. J. Indian Chem. Soc., 1981, 58, 928–929.

  • Sachdev, K. and Kulshreshtha, D. K., Phenolic constituents of Coelogyne ovalis. Phytochemistry, 1986, 25, 499–502.

  • Commenges, D., Scotet, V., Renaud, S., Jacqmin-Gadda, H., Barberger-Gateau, P. and Dartigues, J. F., Intake of flavonoids and risk of dementia. Eur. J. Epidemiol., 2000, 16, 357–363.

  • Knekt, P., Kumpulainen, J., Järvinen, R., Rissanen, H., Heliövaara, M., Reunanen, A. and Aromaa, A., Flavonoid intake and risk of chronic diseases. Am. J. Clin. Nutr., 2002, 76, 560–568.

  • Teixeira, S., Siquet, C., Alves, C., Boal, I., Marques, M. P., Borges, F. and Reis, S., Structure–property studies on the antioxidant activity of flavonoids present in diet. Free Radic. Biol. Med., 2005, 39, 1099–1108.

  • Abe, I., Watanabe, T., Morita, H., Kohno, T. and Noguchi, H., Engineered biosynthesis of plant polyketides: manipulation of chalcone synthase. Org. Lett., 2006, 8, 499–502.

  • Jez, J. M., Bowman, M. E. and Noel, J. P., Expanding the biosynthetic repertoire of plant type III polyketide synthases by altering starter molecule specificity. Proc. Natl. Acad. Sci. USA, 2002, 99, 5319–5324.

  • Ferrer, J. L., Jez, J. M., Bowman, M. E., Dixon, R. A. and Noel, J. P., Structure of chalcone synthase and the molecular basis of plant polyketide biosynthesis. Nature Struct. Mol. Biol., 1999, 6, 775.

  • Ma, W., Wu, Y., Wu, M., Ren, Z. and Zhong, Y., Cloning, characterization and expression of chalcone synthase from medicinal plant Rhus chinensis. J. Plant Biochem. Biotechnol., 2015, 24, 18–24.

  • Helariutta, Y., Elomaa, P., Kotilainen, M., Griesbach, R. J., Schröder, J. and Teeri, T. H., Chalcone synthase-like genes active during corolla development are differentially expressed and encode enzymes with different catalytic properties in Gerbera hybrida (Asteraceae). Plant Mol. Biol., 1995, 28, 47–60.

  • Schröder, J., A family of plant-specific polyketide synthases: facts and predictions. Trends Plant Sci., 1997, 2, 373–378.

  • Kim, S. H., Mizuno, K. and Fujimura, T., Regulated expression of ADP glucose pyrophosphorylase and chalcone synthase during ischolar_main development in sweet potato. Plant Growth Regul., 2002, 38, 173–179.

  • Han, Y. Y., Ming, F., Wang, J. W., Wen, J. G., Ye, M. M. and Shen, D. L., Cloning and characterization of a novel chalcone synthase gene from Phalaenopsis hybrida orchid flowers. Russ. J. Plant Physiol., 2006, 53, 223–230.

  • Wannapinpong, S., Srikulnath, K., Thongpan, A., Choowongkomon, K. and Peyachoknagul, S., Molecular cloning and characterization of the CHS gene family in turmeric (Curcuma longa Linn.). J. Plant Biochem. Biotechnol., 2015, 24, 25–33.


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  • Molecular Docking Study of CHS Gene from a Medicinally Important Orchid, Coelogyne ovalis Lindl.

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Authors

Nutan Singh
Department of Botany, Plant Biotechnology Laboratory, North-Eastern Hill University, Shillong 793 022, India
Suman Kumaria
Department of Botany, Plant Biotechnology Laboratory, North-Eastern Hill University, Shillong 793 022, India

Abstract


Chalcone synthase (CHS) is an important enzyme belonging to the polyketide synthase (type III) family. It is well known for substrate specificity and catalyses diverse groups of polyketides of pharmaceutical value. In the present study, the structure of the CHS protein has been predicted from the medicinal orchid, Coelogyne ovalis Lindl. This is an evergreen orchid, well known for its medicinal uses. The homology-based model was constructed from CHS of C. ovalis (CoCHS) and 16 different ligands were used based on the specificity for molecular docking studies. The four best ligands on the basis of greater negative binding energy were found to be 3-carbomoyl-picoliniyl CoA, followed by carbomoyl-2-napthoyl CoA, p-coumaroyl CoA and malonyl CoA. The present structural study reveals that CoCHS has signature and catalytic amino acid residues, namely Cys165, Asn337, His 306, Phe216 and Phe 266. These residues are known to have a broad-range substrate profile and are responsible for the binding of protein ligands. The present study elucidates the chemical basis of CHS from C. ovalis by understanding the structural and functional relationship. This provides an insight for manipulating the enzymes, CHS-like for the synthesis of new bioactive compounds, which may further enhance the diversity of the polyketide biosynthetic family

Keywords


Coelogyne ovalis, Chalcone Synthase, Ligands, Molecular Docking, Polyketides.

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DOI: https://doi.org/10.18520/cs%2Fv121%2Fi10%2F1323-1327