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Molecular Docking and Dynamics Simulations of Natural Limonoids Interacting with the Nipah Virus Attachment
Victor Moreira de Oliveira1, Márcia Machado Marinho2, Hélcio Silva Dos Santos2,3
1Postgraduate Program in Biotechnology, State University of Ceará, Fortaleza, CE, Brazil.
Introduction:
The Nipah virus (NiV) belongs to the Paramyxoviridae family and is a zoonotic pathogen associated with severe respiratory disease and encephalitis. Fatality rates of up to 70% of diagnosed cases justify its classification as a biosafety level-4 agent. The absence of specific antiviral therapies underscores the urgent need to identify novel molecular inhibitors.
Methods:
This study involved the virtual screening of natural limonoids using molecular docking against the NiV glycoprotein, which is a key target in the adhesion of the virus to human host cells. Subsequently, molecular dynamics simulations were conducted to evaluate the stability of the protein- ligand complexes.
Results:
Molecular docking results showed that desacetylspathelin (DSP) and nimolicinol (NCL) had the most favourable binding free energy (ΔG) values and relevant interactions with residue Leu124. Molecular dynamics simulations revealed greater structural stability for the DSP-containing complex.
Discussion:
The observed interaction profiles suggest that these limonoids, particularly DSP, may interact with the NiV glycoprotein, suggesting a possible influence on virus-host adhesion mechanisms.
Conclusion:
These findings suggest that natural limonoids, particularly DSP, are promising candidates for further investigation as potential Nipah virus glycoprotein modulators/inhibitors and could contribute to the development of antiviral strategies.
Insights
Natural compounds called limonoids, especially desacetylspathelin (DSP), show promise in inhibiting Nipah virus (NiV) glycoprotein interactions. This research could lead to new antiviral treatments for the dangerous NiV infection.
Area of Science:
- Virology
- Drug Discovery
- Computational Chemistry
Background:
- Nipah virus (NiV) is a highly fatal zoonotic pathogen causing severe respiratory illness and encephalitis.
- NiV is classified as a biosafety level-4 agent due to its high mortality rate (up to 70%).
- The lack of specific antiviral treatments necessitates the search for novel inhibitors.
Purpose of the Study:
- To identify natural limonoids that can inhibit Nipah virus glycoprotein.
- To evaluate the potential of these compounds as antiviral agents against NiV.
Main Methods:
- Virtual screening of natural limonoids using molecular docking against the NiV glycoprotein.
- Molecular dynamics simulations to assess the stability of protein-ligand complexes.
Main Results:
- Desacetylspathelin (DSP) and nimolicinol (NCL) exhibited favorable binding free energy with the NiV glycoprotein.
- DSP demonstrated significant structural stability in complex with the NiV glycoprotein.
- Key interactions were observed with residue Leu124.
Conclusions:
- Limonoids, particularly DSP, show potential for modulating NiV glycoprotein activity.
- These compounds may interfere with virus-host adhesion mechanisms.
- DSP is a promising candidate for developing new Nipah virus antiviral strategies.
