DOI: 10.1002/minf.201300185 Interaction of Flaviviruses with Reproduction Inhibitors Binding in b-OG Pocket: Insights from Molecular Dynamics Simulations Evgenia V. Dueva, [a, b, c] Dmitry I. Osolodkin, [a, b, c] Liubov I. Kozlovskaya, [b] Vladimir A. Palyulin,* [a, c] Vladimir M. Pentkovski, [c] and Nikolay S. Zefirov [a] 1 Introduction Design of novel antiviral compounds is one of the most im- portant tasks of contemporary medicinal chemistry. Differ- ent strategies were suggested for solving this problem, and certain successes were achieved. [1] One of prominent antivi- ral drug design strategies is the inhibition of viral fusion – the process of interaction between cellular and viral mem- branes resulting in the release of viral genetic material into the host cell cytoplasm. [2] This strategy was successfully ap- plied to the design of entry inhibitors for HIV, [3] influenza vi- ruses, [2] alphaviruses, [2] and flaviviruses. [4] Nevertheless, mechanisms of the processes underlying fusion inhibition are not sufficiently studied, thus hampering development of this research field. Membrane fusion of enveloped viruses is a complex multi-step process driven by conformational changes of viral envelope proteins. [2,5] Three classes of fusion proteins are known, exemplified by influenza virus, flaviviruses, and vesicular stomatitis virus, for which prefusion and postfu- sion conformations are studied by X-ray crystallography. [6] Flavivirus fusion is of special interest due to the fast rate of this process, [7] making it most suitable for computational studies. The key step in the flavivirus fusion is the pH-de- pendent conformational rearrangement of envelope pro- teins E, which form dimers on the surface of the mature virion. When virus particle interacts with the cellular recep- tors, an endosome is formed enclosing the virion. The en- dosomal pH level of about 6 launches the conformational rearrangements of E proteins, leading to the formation of spikes which attack the endosome membrane. The so-called ‘histidine switch’ hypothesis was proposed to explain the driving force of such rearrangement, which is supposed to be the protonation of histidine residues in the endosome media. [8,9] The movement of E proteins leads to the formation of a membrane stalk and then a mem- brane pore, which allows viral genetic material to be re- leased into the host cell. [2,5,7] Compounds, which bind enve- lope proteins in the sites important for the conformational rearrangement, should prevent fusion, and thus can act as potential antiviral drugs. Abstract : Flaviviral diseases, including dengue fever, West Nile fever, yellow fever, tick-borne encephalitis, Omsk hae- morrhagic fever, and Powassan encephalitis, threaten human health all over the world. Lack of effective antivirals targeting replication cycle of flaviviruses makes the search of such compounds a challenging task. Recently we have identified a reproduction inhibitor effective against tick- borne encephalitis virus and Powassan virus (POWV) (ACS Med. Chem. Lett. , 2013, 4, 869–874). To enable using this in- hibitor as a template for 3D pharmacophore search, a bio- logically active conformation of this molecule should have been established. Here we performed molecular dynamics simulations of the complexes between the different enan- tiomers of the inhibitor and POWV envelope (E) proteins, putative targets of the inhibitor, in the different protona- tion states corresponding to the different stages of mem- brane fusion process. Several stable conformations of the inhibitor were identified, opening routes for further design of more advanced molecules. Keywords: Powassan virus · Flavivirus · Antivirals · Envelope proteins · Molecular dynamics [a] E. V. Dueva, D. I. Osolodkin, V. A. Palyulin, N. S. Zefirov Department of Chemistry, Lomonosov Moscow State University Moscow 119991, Russia phone: + 7-495-939-39-69, fax: + 7-495-939-02-90 *e-mail: vap@qsar.chem.msu.ru [b] E. V. Dueva, D. I. Osolodkin, L. I. Kozlovskaya Chumakov Institute of Poliomyelitis and Viral Encephalitides Moscow 142782, Russia [c] E.V. Dueva, D. I. Osolodkin, V. A. Palyulin, V. M. Pentkovski iScalare Laboratory, Moscow Institute of Physics and Technology Dolgoprudny 141700, Russia Supporting Information for this article is available on the WWW under www.molinf.com. # 2014 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim Mol. Inf. 2014, 33, 695 – 708 695 Full Paper www.molinf.com