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Dengue virus, a small enveloped (+)RNA virus from Flavivirus genus, infects over 100 million people annually, thus representing a global health problem. There is no specific therapy available for the treatment of dengue caused infections and new antivirals are urgently needed. Inhibition of viral entry is an attractive strategy for the development of anti-dengue compounds. Conformational rearrangement of the virus envelope protein (E) from dimeric to trimeric form plays a crucial role in the virus entry process. Small molecule entry inhibitors acting on the E trimer has been found recently. In this work we perform a search of small molecules binding sites on the surface of the E protein trimer using docking. Sites which are more selective to binding of active compounds were identified and analysed. These sites were suggested for the use in virtual screening campaigns in search for the inhibitors of dengue entry process.