Thioaptamers Targeting Dengue Virus Type-2 Envelope Protein Domain III


Journal Title

Journal ISSN

Volume Title



The Dengue Virus Type-2 (DENV-2) is an arbovirus that belongs to the family of Flaviviridae, genus Flavivirus. It includes Dengue virus (DENV) types 1-4, West Nile virus, Langat virus, Omsk hemorrhagic fever virus and others that cause encephalitic or hemorrhagic disease. DENV binds the cell surface receptors and fuses with the host cell membrane using surface envelope protein (E). The E protein ectodomain contains three domains, EDI, EDII and EDIII. The highly immunogenic EDIII is the putative receptor binding domain that also binds neutralizing antibodies. Thus, EDIII is an attractive target for development of vaccines, anti-viral and diagnostic agents.

We have developed leads targeting the DENV-2 EDIII using small molecules and backbone-modified short single stranded DNA molecules called thioaptamers. Thioaptamers are highly resistant to nuclease degradation and do not elicit an immune response. We have identified thioaptamer sequences that bind to DENV-2 EDIII protein with high-affinity. The binding constants were determined for selected thioaptamers using filter binding assays and thermophoresis technique. The apparent Kd ranged from 100 nM to 500 nM. The binding site was determined for thioaptamer DEN TA-1 with DENV-2 EDIII protein using NMR HSQC experiment and mapped on the EDIII structure. Small molecules were selected from a virtual library, through collaboration within our lab, using computational methods that showed tight binding to DENV-2 EDIII protein. Selected molecules were characterized for binding to the EDIII target using protein thermal stability shift assay and 2-D HSQC NMR experiment. The apparent binding affinity for one of the selected compounds was calculated to be around 500 µM.

The selected thioaptamers can be modified by attaching the selected small molecule binder at specific positions along the sequence using amide coupling reaction to create a novel class of X-aptamer library. The X-aptamer sequence with modification at the right positions can be selected that can specifically bind the DENV-2 EDIII target with very high affinity. These molecules can potentially be developed as a therapeutic or vaccine against dengue virus.



Dengue virus, Envelope protein domain 3, selection of thioaptamers, biophysical methods for characterization of binding, small molecule selection, X-aptamer development