Can Modern Molecular Modeling Methods Help Find the Area of Potential Vulnerability of Flaviviruses?

International Journal of Molecular Sciences. 2022. Vol. 23. No. 14. Article 7721.

Shanshin D., Borisevich S., Bondar A., Yuri B. Porozov, Rukhlova E., Protopopova E., Ushkalenko N., Loktev V., Chapoval A., Ilyichev A., Shcherbakov D.

Flaviviruses are single-stranded RNA viruses that have emerged in recent decades and infect up to 400 million people annually, causing a variety of potentially severe pathophysiological processes including hepatitis, encephalitis, hemorrhagic fever, tissues and capillaries damage. The Flaviviridae family is represented by four genera comprising 89 known virus species. There are no effective therapies available against many pathogenic flaviviruses. One of the promising strategies for flavivirus infections prevention and therapy is the use of neutralizing antibodies (NAb) that can disable the virus particles from infecting the host cells. The envelope protein (E protein) of flaviviruses is a three-domain structure that mediates the fusion of viral and host membranes delivering the infectious material. We previously developed and characterized 10H10 mAb which interacts with the E protein of the tick-borne encephalitis virus (TBEV) and many other flaviviruses' E proteins. The aim of this work was to analyze the structure of E protein binding sites recognized by the 10H10 antibody, which is reactive with different flavivirus species. Here, we present experimental data and 3D modeling indicating that the 10H10 antibody recognizes the amino acid sequence between the two cysteines C92-C116 of the fusion loop (FL) region of flaviviruses' E proteins. Overall, our results indicate that the antibody-antigen complex can form a rigid or dynamic structure that provides antibody cross reactivity and efficient interaction with the fusion loop of E protein.

Keywords: monoclonal antibody, ELISA, flavivirus, TBEV, WNV, ZIKV, DENV, recombinant protein, molecular protein docking, molecular protein dynamics