Rupintrivir is a promising candidate for treating severe cases of Enterovirus-71 infection

Abstract

Aim: To evaluate the suitability of rupintrivir against Enterovirus 71 (EV71) induced severe clinical symptoms using computational methods.

Methods: The structure of EV71 3C protease was predicted by homology modeling. The binding free energies between rupintrivir and EV71 3C and human rhinovirus 3C protease were computed by molecular dynamics and molecular mechanics Poisson-Boltzmann/surface area and molecular mechanics generalized-born/surface area methods. EV71 3C fragments obtained from clinical samples collected during May to July 2008 in Shanghai were amplified by reverse-transcription and polymerase chain reaction and sequenced.

Results: We observed that rupintrivir had favorable binding affinity with EV71 3C protease (-10.76 kcal/mol). The variability of the 3C protein sequence in isolates of various outbreaks, including those obtained in our hospital from May to July 2008, were also analyzed to validate the conservation of the drug binding pocket.

Conclusion: Rupintrivir, whose safety profiles had been proved, is an attractive candidate and can be quickly utilized for treating severe EV71 infection.

Figure 1

Chemical structure of rupintrivir.

Figure 2

Sequence alignment of EV71 3C protease with HRV 3C (1CQQ) and Poliovirus 3C (1L1N). Secondary structures (α helixes and β sheets) were illustrated.

Figure 3

The overall structure of EV71 3C protease complexed with rupintrivir. A: A solid ribbon presentation of EV71 3C with rupintrivir; B: 90° rotation view of the structure.

Figure 4

Receptor and ligand backbone displacement. A: Backbone root mean square deviation (RMSD) of the HRV 3C (1CQQ) and EV71 3C protein; B: Ligand backbone RMSD during the 2ns molecular dynamics simulation.

Figure 5

Binding mode of AG7088 with 1CQQ (A) and EV71 3C (B). The protein surface is rendered semitransparent with associated backbone and side chain atom.

Figure 6

Energy decomposition (using MM-GBSA) of the key interaction residues in 1CQQ and EV71 3C complexes.

Figure 7

Sequence variability of EV71 3C protease and its effect on rupintrivir binding (A) Phylogenetic tree of 48 isolates of EV71 in various outbreaks. (B) A colored representation of sequence variation on the surface of 3C protease. Positions with two, three and over three different residues are labeled green, yellow and red, respectively. Residue Ser 128 and Thr 142 were labeled.

Figure 8

Sequence alignment of 3C protease from isolates collected in various epidemics (CHN: Mainland China; TW: Taiwan, China; FY: Fuyang, Anhui Province, China; SHZN: Shenzhen, China; AUS: Australia; SAR, SIN, MAL: Malaysia; KOR: Korea; NO: Norway). Residues important for rupintrivir are labeled with red open boxes.