Molecular docking and dynamic studies of crepiside E beta glucopyranoside as an inhibitor of snake venom PLA2

  • Mala S. KumarEmail author
  • Amjesh R.
  • Silpa Bhaskaran
  • Delphin R. D.
  • Achuthsankar S. Nair
  • Sudhakaran P. R.
Original Paper


Alternative treatments from plant-derived small molecules for neutralizing the venom lethality in snake envenomation are prevalent now. Elephantopus scaber, a tropical plant species has been recognized for its various pharmacological activities and especially anti-snake venom property; however, the molecular basis for this property is not understood. It is reported that snake venom PLA2 is a toxic factor with pharmacological effects independent of their catalytic activity. Here we report the inhibition of catalytic property of Cobra and Viper (group I and group II) snake venom PLA2 by the phytocompounds from E. scaber through molecular docking and dynamics studies. Initially, Lipinski’s rule, ADMET, and molecular docking studies were carried out. Our results show that among 124 phytocompounds, crepiside E (deacylcynaropicrin-3′ beta-glucopyranoside) has shown interactions with the conserved catalytic active site residues, His 48 and Asp 49, in both the PLA2s. Further, molecular dynamic simulations for 60 ns confirmed the stability of crepiside E in the active site of PLA2s and were found to be stable throughout the simulation. In order to understand the drug-likeness of crepiside E, pIC50 and MMGBSA scores were correlated by performing a linear regression analysis. Crepiside E was found to have similar chemical features to that of doxycycline, a known PLA2 inhibitor as indicated by a similarity score of 64.15%. Hence, it is concluded that crepiside E beta glucopyranoside present in Elephantopus scaber contributes to neutralizing the snake venom.


Elephantopus scaber Snake envenomation PLA2 Crepiside E MMGBSA-pIC50 correlation Molecular docking and dynamics 



This work was supported by the Centre for Excellence in Ayur-Informatics and Computer Aided Drug Design through FAST Scheme under MHRD (No. F. 5-6/2013-TS.VII) is gratefully acknowledged. The computational facilities were provided by the Department of Computational Biology and Bioinformatics, University of Kerala is also acknowledged. The authors would also like to sincerely thank Saraswathy V., Research Scholar, Department of Computational Biology and Bioinformatics, University of Kerala for her valuable suggestions and comments.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Supplementary material

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Mala S. Kumar
    • 1
    Email author
  • Amjesh R.
    • 1
  • Silpa Bhaskaran
    • 1
  • Delphin R. D.
    • 1
  • Achuthsankar S. Nair
    • 1
  • Sudhakaran P. R.
    • 1
  1. 1.Department of Computational Biology and Bioinformatics, KaryavattomUniversity of KeralaThiruvananthapuramIndia

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