Structure-based identification of small-molecule inhibitors that target the DIII domain of the Dengue virus glycoprotein E pan-serotypically

Abstract

Dengue viral infection is caused by the Dengue virus, which spreads to humans through the bite of infected mosquitos. Dengue affects over half of the global population, with an estimated 500 million infections per year. Despite this, no effective treatment is currently available, however, several promising candidates are undergoing pre-clinical/clinical testing. The existence of four major serotypes is an important challenge in the development of drugs and vaccines to combat Dengue virus infection. Hence, the drug/vaccine thereby developed should neutralize all the four serotypes equally. However, there is no pan-serotype specific treatment for Dengue virus, thereby emphasizing the need for the identification of novel drug-like compounds that can target all serotypes of the Dengue virus equally. To this end, we employed virtual screening methodologies to find drug-like compounds that target the domain III of glycoprotein E. Most importantly, domain III of E protein is involved in viral fusion with the host membrane and is also targeted by neutralizing antibodies. Our study found two small molecule drug-like compounds (out of the 3 million compounds screened) having similar binding affinity with all four serotypes. The compounds thereby identified exhibit favourable drug like properties and can be developed as a treatment for Dengue virus.

Fig 1. Conservation in domain III among Dengue virus serotypes, sequence and structural comparison, and its interaction with mAb 4E11.

(a) Multiple sequence alignment of Domain III from Dengue virus serotypes (Dengue virus 1, Dengue virus 2, Dengue virus 3, and Dengue virus 4). The sequence alignment was done using ESPript (https://espript.ibcp.fr). (b) The 3D structural alignment of Domain III from Dengue virus serotypes, highlighting conserved structural elements. Dengue virus 1 is shown in magenta, Dengue virus 2 in blue, Dengue virus 3 in orange, Dengue virus 4 in green. (c) The interaction between Domain III and Monoclonal Antibody 4E11. The DIII structure is shown in light orange, mAb 4E11 in pale cyan and residues involved in the binding in blue.

Fig 2. Identification of small molecules through high-throughput virtual screening.

The Venn diagram illustrating the distribution of compounds identified across different Dengue virus serotypes (Dengue virus 1, Dengue virus 2, Dengue virus 3, and Dengue virus 4). The overlapping regions indicate compounds shared between two or more serotypes, while unique regions represent compounds exclusive to a particular serotype.

Fig 3. The chemical structures of lead molecules, and the structural relationships among these potential antiviral agents for Dengue virus.

(a) The molecular structures of lead compounds identified as top binders to the Domain III (DIII) of the Dengue virus E protein for each serotype. The compounds belong to two main classes: Nucleotide analogues (148197, 191763, 133406, 10705, 17473) and phenol ether (8296). (b) Structural superimposition of the lead molecules identified from DIII binding for Dengue virus 1 (magenta), Dengue virus 2 (blue), Dengue virus 3 (orange), and Dengue virus 4 (green). Note identified small molecules bind at similar region across the serotypes.

Fig 4

Molecular docking results of the DIII domain of Dengue virus 1–4 (left to right) with lead compounds (a) 8296 (b) 10705 at the active site of interaction. Atoms are coloured as follows: Nitrogen is blue, oxygen is red, carbon is black, sulphur is yellow, phosphorus is purple, and hydrophobic residues are brick red. Similarly, grey bonds represent ligand bonds, orange: Non-ligand bonds, olive green: Hydrogen bonds, red: Salt bridges, and brick red: Hydrophobic interactions.

Fig 5. MD simulations of domain III in presence of compound 8296 and 10705.

(a) The C^α backbone RMSD values over time, reflecting the deviation of the simulated structure from the starting reference structure for compound 8296 (left panel) and 10705 (right panel). (b) The RMSF values for individual residues, highlighting the degree of fluctuation or flexibility during the simulation. Higher RMSF values indicate more flexible regions, while lower values suggest relatively stable regions. Binding site residues show remarkably low RMSF fluctuations suggesting stable interaction between the compound and the protein. The DIII domain of Dengue virus 1, 2, 3, and 4 are shown in magenta, black, green, and blue, respectively. The interacting region is highlighted in a box.