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Table 2 Calculated poses (FlexX 2.0) and estimated binding affinity calculated with HYDE module (FlexX) for the drugs BIT225, amantadine, rimantadine and N N-DNJ

From: Computational modeling of the p7 monomer from HCV and its interaction with small molecule drugs

Compound Time   No loop     Loop     TMD11-32  
ScoreF ScoreH ScoreF ScoreH ScoreF ScoreH
[kJ/mol] [kJ/mol] [kJ/mol] [kJ/mol] [kJ/mol] [kJ/mol]
BIT225 0 −16.7 −21.7 −21.6 −16.5   
−13.7 −15.9 −16.8 1.4   
  −12.6 −6.7 −13.9 −9.8   
150 −17.7 −14.4 −23.8 −27.0 −14.3 −8.5
  −16.2 −16.4 −20.2 −14.4 −12.1 −13.4
  −13.9 −15.9    −11.1 −8.6
ssAmatadine 0 1.4 −2.7 −5.0 −9.3   
    −0.5 −10.8   
150 −2.3 −8.5 −3.7 −5.7 −2.0 −9.9
  −1.6 0.6 −3.0 −3.8 −0.5 −8.0
Rimantadine 0 −3.7 −2.4 −4.8 −7.9   
  −3.1 −10.0 −4.2 −2.4   
  −1.6 −8.1 −2.6 −7.7   
150 −2.8 −15.6 −4.7 −10.1 −3.8 −15.9
  −1.9 −7.0 −4.6 −7.2 −1.2 −12.6
  −1.6 −15.0 −3.8 −12.4 −0.9 −7.4
N N-DNJ 0 −2.0 −8.2 −7.8 −16.1   
  −1.1 −21.9     
150 −0.9 −8.0 −7.1 −8.9 2.5 −21.3
  −0.3 −39.3 −4.1 −14.6 2.9 −20.7
      4.8 −11.2
  1. The energies of the best poses of each cluster are shown for the respective structures at 0 ns and 150 ns (Time). All values are given in kJ/mol. ‘ScoreF’ refers to the values from FlexX 2.0, ‘scoreH’ to those from HYDE.