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Potentiality of bioactive compounds as inhibitor of M protein and F protein function of human respiratory syncytial virus

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Abstract

The human respiratory syncytial virus (RSV) creates a pandemic every year in several countries in the world. Lack of target therapeutics and absence of vaccines have prompted scientists to create novel vaccines or small chemical treatments against RSV's numerous targets. The matrix (M) protein and fusion (F) glycoprotein of RSV are well characterized and attractive drug targets. Five bioactive compounds from Alnus japonica (Thunb.) Steud. were taken into consideration as lead compounds. Drug-likeness characters of them showed the drugs are non-toxic and non-mutagenic and mostly lipophobic. Molecular docking reveals that all bioactive compounds have better binding and better inhibitory effect than ribavirin which is currently used against RSV. Praecoxin A appeared as the best lead compound between them. It creates 7 different types of bonds with amino acids of M protein and 5 different types of bonds with amino acids of F protein. Van der Waals interactions highly influenced the binding energies. Molecular dynamic simulations represent the non-deviated and less fluctuating nature of praecoxin A. Principal Component Analysis showed praecoxin A complex with RSV matrix protein is more stable than ribavirin complex. This study will help to develop a new drug to inhibit RSV. All ligands were minimized through semi-empirical PM3 process with MOPAC. Toxicity was tested by ProTox-II server. Molecular docking studies were carried out using AutoDock 4.2. Molecular dynamics simulations for 100 ns were carried out through GROMACS 5.12 MD and GROMOS96 43a1 force field. The graphs were produced by GROMACS's XMGrace program.

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Acknowledgements

The authors are grateful to Bioinformatics Facility, Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, India, for the provision of computational support. The work was partially conducted in the context of the Bioinformatics Resources and Applications Facility (BRAF), C-DAC, Pune, India.

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  1. Department of Microbiology, Raiganj University, Raiganj, West Bengal, 733134, India

    Debanjan Mitra & Pradeep K. Das Mohapatra

  2. Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, Odisha, 757003, India

    Manish Paul & Hrudayanath Thatoi

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Contributions

DM conceived and designed the project. PKDM conducted initial manual verifications. Target protein and ligand compounds were identified by DM Molecular docking was performed by DM Molecular dynamic simulations were performed by MP and HT Analysis of those results was done by DM Draft of the manuscript was prepared by DM and MP Final version of the manuscript was edited by HT The whole work was done under the supervision of PKDM.

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Correspondence to Pradeep K. Das Mohapatra.

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Mitra, D., Paul, M., Thatoi, H. et al. Potentiality of bioactive compounds as inhibitor of M protein and F protein function of human respiratory syncytial virus. In Silico Pharmacol. 12, 5 (2024). https://doi.org/10.1007/s40203-023-00178-w

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