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Exploring Chemical Space to Identify Partial Binders Against hMPV Nucleocapsid Protein
Monika Verma1, Nikita S Panchal2, Pramod Kumar Yadav1
1Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, Uttar Pradesh, India.
Researchers identified two natural compounds, M1 and M3, as potential inhibitors for human metapneumovirus (hMPV) by targeting its nucleocapsid protein. These findings offer new therapeutic avenues for respiratory infections caused by hMPV.
Area of Science:
- Virology
- Structural Biology
- Computational Chemistry
Background:
- Human metapneumovirus (hMPV) is a significant cause of acute respiratory tract infections, particularly in vulnerable populations like children and the elderly.
- hMPV infection can be recurrent in immunocompromised individuals and typically acquired by age five.
- The hMPV nucleocapsid (N) protein is crucial for viral RNA protection and represents a promising therapeutic target.
Purpose of the Study:
- To identify potential natural inhibitors of the hMPV nucleocapsid protein.
- To evaluate the binding affinity and interactions of identified compounds with the hMPV nucleoprotein.
Main Methods:
- Structure-based virtual screening of the ZINC Database.
- Molecular dynamics simulations (250-ns scale).
- Analysis of docking scores, binding site interactions, and molecular dynamics trajectories.
Main Results:
- Two natural molecules, M1 (ZINC85629735) and M3 (ZINC85569125), exhibited high binding affinity to the hMPV nucleoprotein.
- M1 and M3 showed favorable docking scores (-9.6 and -10.7 kcal/mol) and MMGBSA binding energies (-81.94 and -99.63 kcal/mol).
- Molecular dynamics simulations confirmed the stability and binding potential of these compounds.
Conclusions:
- M1 and M3 demonstrate significant potential as therapeutic agents against hMPV.
- These compounds show promising attributes for inhibiting hMPV replication by targeting the nucleocapsid protein.
