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

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Abstract

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.

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Acknowledgements

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.

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  1. Department of Computational Biology and Bioinformatics, Karyavattom, University of Kerala, Thiruvananthapuram, Kerala, 695581, India

    Mala S. Kumar, Amjesh R., Silpa Bhaskaran, Delphin R. D., Achuthsankar S. Nair & Sudhakaran P. R.

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Kumar, M.S., R., A., Bhaskaran, S. et al. Molecular docking and dynamic studies of crepiside E beta glucopyranoside as an inhibitor of snake venom PLA2. J Mol Model 25, 88 (2019). https://doi.org/10.1007/s00894-019-3954-2

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