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Molecular docking and simulation studies of Phyllanthus amarus phytocompounds against structural and nucleocapsid proteins of white spot syndrome virus

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Abstract

White spot disease caused by white spot syndrome virus (WSSV) is a lethal disease for shrimp. Envelope structural proteins play a major role in viral attachment and are believed to be the initial molecules to interact with the host cell. Thus, the envelope proteins have been preferred as a potential molecular target for drug discovery. In the present investigation, molecular docking and simulation analysis were performed to predict the binding efficiency of phytocompounds identified from Phyllanthus amarus with major envelope proteins, VP26, VP28, and VP110, and a nucleocapsid protein VP664 of WSSV. The docking result reveals that the compounds 2H-1-benzopyran-6-ol, 3,4-dihydro-2,5,7,8-tetramethyl-2-(4,8,12-trimethyltridecyl)-acetate and 1,4-benzenediamine, N,N′-diphenyl exhibited highest binding energy with the envelope proteins. The mobility of protein–ligand binding complex at various time intervals was validated by molecular dynamics and simulation study. Therefore, P. amarus phytocompounds were found to be most suitable inhibitors for the antiviral treatment for WSSV infection.

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References

  • Al-Hazmi NA (2010) Fungal isolates and their toxicity from different ecosystems in Jeddah, Saudi Arabia. Afr J Biotechnol 9(34):5590–5598

    CAS  Google Scholar 

  • Berendsen HJC, van der Spoel D, van Drunen R (1995) GROMACS: a message-passing parallel molecular dynamics implementation. Comput Phys Commun 91:43–56

    Article  CAS  Google Scholar 

  • Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28(1):235–242

    Article  CAS  Google Scholar 

  • Cash GG (1998) Prediction of chemical toxicity to aquatic organisms: ECOSAR vs. Microtox® assay. Environ Toxicol 3(3):211–216

    Google Scholar 

  • Chakraborty S, Ghosh U, Balasubramanian T, Das P (2014) Screening, isolation and optimization of anti-white spot syndrome virus drug derived from marine plants. Asian Pac J Trop Biomed 4:S107–S117

    Article  Google Scholar 

  • Eisenberg D, Lüthy R, Bowie JU (1997) VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 277:396–404

    Article  CAS  Google Scholar 

  • Ghosh U, Chakraborty S, Balasubramanian T, Das P (2014) Screening, isolation and optimization of anti–white spot syndrome virus drug derived from terrestrial plants. Asian Pac J Trop Biomed 4:S118–S128

    Article  Google Scholar 

  • Islam AKMN, Ali MA, Sayeed A, Salam SMA, Islam A, Rahman M, Khan GRMA, Khatun S (2003) An antimicrobial terpenoid from Caesalpinia pulcherrima Swartz: its characterisation, antimicrobial and cytotoxic activities. Asian J Plant Sci 2(17–24):1162–1165

    Google Scholar 

  • Joseph J, Bhaskaran R, Kaliraj M, Muthuswamy M, Suresh A (2017) Molecular Docking of Phytoligands to the viral protein receptor P. monodon Rab7. Bioinformation 13(4):116–121

    Article  Google Scholar 

  • Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26(2):283–291

    Article  CAS  Google Scholar 

  • Leu JH, Tsai JM, Wang HC, Wang AHJ, Wang CH, Kou GH, Lo CF (2005) The unique stacked rings in the nucleocapsid of the white spot syndrome virus virion are formed by the major structural protein VP664, the largest viral structural protein ever found. J Virol 79(1):140–149

    Article  CAS  Google Scholar 

  • Leu JH, Yang F, Zhang X, Xu X, Kou GH, Lo CF (2009) Whispovirus. Curr Top Microbiol Immunol 328:197–227

    CAS  Google Scholar 

  • Meyer BN, Ferrign RN, Putnam JE, Jacobson LB, Nicholas DE, McLaughlin JL (1982) Brine shrimp: a convenient general bioassay for active plant constituents. Planta Med 45:31–34

    Article  CAS  Google Scholar 

  • Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30:2785–2791

    Article  CAS  Google Scholar 

  • Musthaq SKS, Kwang J (2015) Reprint of “Evolution of specific immunity in shrimp—a vaccination perspective against white spot syndrome virus”. Dev Comput Immunol 48(2):342–353

    Article  Google Scholar 

  • Patel JR, Tripathi P, Sharma V, Chauhan NS, Dixit VK (2011) Phyllanthus amarus: ethnomedicinal uses, phytochemistry and pharmacology: a review. J Ethnopharmacol 138(2):286–313

    Article  CAS  Google Scholar 

  • Price KS, Waggy GT, Conway RA (1974) Brine shrimp bioassay and seawater BOD of petrochemicals. J Water Pollut Control Fed 46:63–77

    CAS  Google Scholar 

  • Rahmatullah M, Sadeak SMI, Bachar SC, Hossain MT, Abdullah-al-Mamun, Montaha Jahan N, Chowdhury MH, Jahan R, Nasrin D, Rahman M, Rahman S (2010) Brine shrimp toxicity study of different Bangladeshi medicinal plants. Adv Nat Appl Sci 4(2):163–173

    Google Scholar 

  • Sanchez-Paz A (2010) White spot syndrome virus: an overview on an emergent concern. Vet Res 41(6):43

    Article  Google Scholar 

  • SchuÈttelkopf AW, Van Aalten DMF (2004) PRODRG: a tool for high-throughput crystallography of protein–ligand complexes. Acta Cryst D60:1355–1363

    Google Scholar 

  • Sivakumar KC, Sajeevan TP, Singh IB (2016) Marine derived compounds as binders of the White spot syndrome virus VP28 envelope protein: in silico insights from molecular dynamics and binding free energy calculations. Comput Biol Chem 64:359–367

    Article  CAS  Google Scholar 

  • Sorgeloos P, Remiche-Van Der Wielen C, Persoone G (1978) The use of Artemia nauplii for toxicity tests—a critical analysis. Ecotoxicol Environ Saf 2:249–255

    Article  CAS  Google Scholar 

  • Sudharsana S, Rajashekar Reddy CB, Dinesh S, Rajasekhara Reddy S, Mohanapriya A, Itami T, Sudhakaran R (2016) Molecular docking and simulation studies of 3-(1-chloropiperidin-4-yl)-6-fluoro benzisoxazole 2 against VP26 and VP28 proteins of white spot syndrome virus. J Fish Dis 39:1231–1238

    Article  CAS  Google Scholar 

  • Sundaram D, Kesavan K, Kumaravel H, Mohammed RF, Tohru M, Toshiaki I, Raja S (2016) Protective efficacy of active compounds from Phyllanthus amarus against white spot syndrome virus in freshwater crab (Paratelphusa hydrodomous). Aquac Res 47:2061–2067

    Article  Google Scholar 

  • Tang X, Wu J, Sivaraman J, Hew CL (2007) Crystal structures of major envelope proteins VP26 and VP28 from white spot syndrome virus shed light on their evolutionary relationship. J Virol 81(12):6709–6717

    Article  CAS  Google Scholar 

  • The UniProt Consortium (2015) UniProt: a hub for protein information. Nucleic Acids Res 43:D204–D212

    Article  Google Scholar 

  • Thompson M (2004) Molecular docking using ArgusLab, an efficient shape-based search algorithm and the AScore scoring function. In: ACS meeting. Philadelphia. 172, CINF 42: PA

  • Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y (2015) The I-TASSER Suite: protein structure and function prediction. Nat Methods 12(1):7–8

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors are thankful to Prof. A.S. Sahul Hameed of C. Abdul Hakeem College, Tamil Nadu, India, for providing the virus stock to perform the studies. The authors are grateful to the management of VIT University for providing necessary facilities to carry out this study.

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Authors and Affiliations

  1. Aquaculture Biotechnology Laboratory, School of Biosciences and Technology, VIT University, Vellore, 632 014, Tamil Nadu, India

    S. Dinesh & R. Sudhakaran

  2. Bioinformatics Division, School of Biosciences and Technology, VIT University, Vellore, 632 014, Tamil Nadu, India

    S. Sudharsana & A. Mohanapriya

  3. Faculty of Agriculture, University of Miyazaki, 1-1, GakuenKibanadai-nishi, Miyazaki, 889-2192, Japan

    T. Itami

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  1. S. Dinesh
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  2. S. Sudharsana
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  3. A. Mohanapriya
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  4. T. Itami
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  5. R. Sudhakaran
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Correspondence to R. Sudhakaran.

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Dinesh, S., Sudharsana, S., Mohanapriya, A. et al. Molecular docking and simulation studies of Phyllanthus amarus phytocompounds against structural and nucleocapsid proteins of white spot syndrome virus. 3 Biotech 7, 353 (2017). https://doi.org/10.1007/s13205-017-0938-8

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