2. Academic Validation
  3. Dynamics of natural product Lupenone as a potential fusion inhibitor against the spike complex of novel Semliki Forest Virus

Dynamics of natural product Lupenone as a potential fusion inhibitor against the spike complex of novel Semliki Forest Virus

  • PLoS One. 2022 Feb 25;17(2):e0263853. doi: 10.1371/journal.pone.0263853.
Nobendu Mukerjee 1 2,  Anubhab Das 1,  Swastika Maitra 3,  Arabinda Ghosh 4,  Prattusha Khan 5,  Athanasios Alexiou 6 7,  Abhijit Dey 8,  Debabrat Baishya 9,  Faizan Ahmad 10,  Punya Sachdeva 11,  Muhanna K Al-Muhanna 12
Affiliations

Affiliations

  • 1 Department of Microbiology, Ramakrishna Mission Vivekananda Centenary College, West Bengal, India.
  • 2 Department of Health Sciences, Novel Global Community Educational Foundation, Hebersham, NSW, Australia.
  • 3 Department of Microbiology, Adamas University, Kolkata, India.
  • 4 Microbiology Division, Department of Botany, Gauhati University, Guwahati, Assam, India.
  • 5 Department of Microbiology, St. Xavier's Autonomous College, Kolkata, India.
  • 6 Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW, Australia.
  • 7 AFNP Med Austria, Wien, Austria.
  • 8 Department of Life Sciences, Presidency University, Kolkata, West Bengal, India.
  • 9 Department of Bioengineering and Technology, GUIST, Gauhati University, Guwahati, Assam, India.
  • 10 Department of Medical Elementology and Toxicology, Jamia Hamdard, Delhi, India.
  • 11 Amity Institute of Neuropsychology and Neurosciences, Amity University, Noida, India.
  • 12 The Material Science Research Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia.
PMID: 35213606 DOI: 10.1371/journal.pone.0263853
Abstract

The Semliki Forest Virus (SFV) is an RNA virus with a positive-strand that belongs to the Togaviridae family's Alphavirus genus. An epidemic was observed among French troops stationed in the Central African Republic, most likely caused by the SFV virus. The two transmembrane proteins El and E2 and the peripheral protein E3 make up the viral spike protein. The virus binds to the host cell and is internalized via endocytosis; endosome acidification causes the E1/E2 heterodimer to dissociate and the E1 subunits to trimerize. Lupenone was evaluated against the E1 spike protein of SFV in this study based on state-of-the-art cheminformatics approaches, including molecular docking, molecular dynamics simulation, and binding free energy calculation. The molecular docking study envisaged major interactions of Lupenone with binding cavity residues involved non-bonded van der Waal's and Pi-alkyl interactions. Molecular dynamic simulation of a time scale 200 ns corroborated interaction pattern with molecular docking studies between Lupenone and E1 spike protein. Nevertheless, Lupenone intearcation with the E1 spike protein conforming into a stable complex substantiated by free energy landscape (FEL), PCA analysis. Free energy decomposition of the binding cavity resdiues of E1 spike protein also ensured the efficient non-bonded van der Waal's interaction contributing most energy to interact with the Lupenone. Therefore, Lupenone interacted strongly at the active site conforming into higher structural stability throughout the dynamic evolution of the complex. Thus, this study perhaps comprehend the efficiency of Lupenone as lead molecule against SFV E1 spike protein for future therapeutic purpose.

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