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Whether Molecular Dynamics Methods Can Explain Different Activities of Stereoisomers Against Respiratory Syncytial Virus or Not?

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Abstract

The antiviral activity of monoterpene-aryl coumarin conjugates depends on the absolute configuration of the monoterpene moiety, which seems to be due to different arrangements of compounds at the binding site of the F-protein of respiratory syncytial virus - the supposed target for these compounds. Molecular dynamics and metadynamics methods make it possible to estimate the difference in the nature of the interaction between stereoisomers and key amino acid residues of the binding site and to explain their different antiviral activity.

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Notes

  1. ΔGMM–GBSA is the free Gibbs energy. GBSA is the generalized Born model (GB) augmented with the surface area available for a hydrophobic solvent (SA).

  2. D is the aspartic acid, F-protein is glycoprotein, surface RSV protein, F is phenylalanine, L is leucine, Q is glutamine.

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Funding

The authors acknowledge the support of the Russian Science Foundation (grant No. 21-13-00026).

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Authors and Affiliations

  1. Ufa Institute of Chemistry, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, Russia

    S. S. Borisevich

  2. Institute of Intellectual Cybernetic Systems, National Research Nuclear University, Moscow Engineering Physics Institute, Moscow, Russia

    S. S. Borisevich

  3. Vorozhtsov Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia

    K. P. Volcho & N. F. Salakhutdinov

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  1. S. S. Borisevich
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Correspondence to S. S. Borisevich.

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Russian Text © The Author(s), 2024, published in Zhurnal Strukturnoi Khimii, 2024, Vol. 65, No. 1, 120491.https://doi.org/10.26902/JSC_id120491

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Borisevich, S.S., Volcho, K.P. & Salakhutdinov, N.F. Whether Molecular Dynamics Methods Can Explain Different Activities of Stereoisomers Against Respiratory Syncytial Virus or Not?. J Struct Chem 65, 82–91 (2024). https://doi.org/10.1134/S0022476624010086

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