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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.