Author Archives: Lucia

Docking rigido

Il target scelto è la porzione F(1)-ATPase mitocondriale del bovino, il pdb 2JIZ è dell’enzima inibito dal resveratrolo.

Link al paper: Mechanism of inhibition of bovine F1-ATPase by resveratrol and related polyphenols.

I ligandi sono:

5 azo attivi (A1-A2-A3-A4-A5)

2 azo non attivi (B10-B11)

2 noti inibitori dell’ATPase (RES=resveratrolo, PIT= piceatannolo).

Il file yob di ogni molecola è stato salvato con questo nome: F1-2jiz_ligand.yob

La macro usata è: dock_run_Lucia_ATPSynt.mcr

Risultati

Binding energy[kcal/mol]

Ligandi

A1

A2

A3

A4

A5

B10

B11

PIT

RES

Valore di Binding dei primi 3 cluster 8,907 9,463 9,104 9,030 9,627 8,803 9,827 9,266 9,128
8,814 9,450 9,093 8,670 9,504 8,672 9,550 9,242 9,027
8,677 9,449 9,082 8,557 9,400 8,464 8,616 8,571 8,211
Media 8,799 9,454 9,093 8,752 9,510 8,646 9,331 9,026 8,789

Correlazione Binding energy/MIC50

C. albicans S. aureus Binding
A1 15 17 9,51 =(8,799-8,4)/0,084*2
A2 12 15 25,10 =(9,454-8,4)/0,084*2
A3 3,5 7 16,50 =(9,093-8,4)/0,084*2
A4 5 10 8,39 =(8,752-8,4)/0,084*2
A5 3 7 26,44 =(9,510-8,4)/0,084*2
B10 30 30 5,87 =(8,646-8,4)/0,084*2
B11 30 30 22,17 =(9,331-8,4)/0,084*2
PIT 14,91 =(9,026-8,4)/0,084*2
RES 9,25 =(8,789-8,4)/0,084*2

Il file yob di ogni

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molecola è stato salvato con questo nome: F1-2jiz_ligand.yob

  • La macro usata è: dock_run_Lucia_ATPSynt.mcr

 

Risultati

Binding energy[kcal/mol]

Ligandi

A1

A2

A3

A4

A5

B10

B11

PIT

RES

Valore di Binding dei primi 3 cluster 8,907 9,463 9,104 9,030 9,627 8,803 9,827 9,266 9,128
8,814 9,450 9,093 8,670 9,504 8,672 9,550 9,242 9,027
8,677 9,449 9,082 8,557 9,400 8,464 8,616 8,571 8,211
Media 8,799 9,454 9,093 8,752 9,510 8,646 9,331 9,026 8,789

 

Correlazione Binding energy/MIC50

C. albicansug/mL S. aureusug/mL Binding[kcal/mol]
A1 15 17 9,51 =(8,799-8,4)/0,084*2
A2 12 15 25,10 =(9,454-8,4)/0,084*2
A3 3,5 7 16,50 =(9,093-8,4)/0,084*2
A4 5 10 8,39 =(8,752-8,4)/0,084*2
A5 3 7 26,44 =(9,510-8,4)/0,084*2
B10 30 30 5,87 =(8,646-8,4)/0,084*2
B11 30 30 22,17 =(9,331-8,4)/0,084*2
PIT 14,91 =(9,026-8,4)/0,084*2
RES 9,25 =(8,789-8,4)/0,084*2

 

http://www.atpsynthase.info/FAQ.html

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composition of ATP synthase

 

Matrice M1

A3

A5

PLA

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4060D + TWEEN 80 al 10 %0.45+0.05= 0.5 g

0.01 0.05 0.1 0.5 1 0.01 0.05 0.1 0.5 1
0.05mg 0.25mg 0.5mg 2.5mg 5mg 0.05mg 0.25mg 0.5mg 2.5mg 5mg
Preparando una soluzione 9 mgAzo/9mL Acetone
50µL 250µL 500µL 2.5mL 5mL 50µL 250µL 500µL 2.5mL 5mL

 

Il film di PLA 4060D + TWEEN 80 non è solubile in

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acqua.

MATERIALI:

  • Polylactide Acid (NatureWorks® Ingeo™ 4060D Sealant Grade PLA) (http://www.matweb.com/search/datasheet.aspx?matguid=46b73a0a9abe4e63aa37cfa6bb785644&ckck=1)
  • TWEEN® 80
  • Chloroform
  • Azo (A3-A5)

 

Preparazione matrice

La matrice è composta dal 10 % di Tween80 e 90% di PLA ha un peso totale di 6g, i polimeri sono stati solubilizzati in 120 mL di CHCl3 sotto agitazione magnetica a temperatura ambiente per 5 ore. La matrice risultante viene divisa in aliquote da 15,00 g, che corrispondono al peso di matrice impiegata per colare ogni singolo film. Vengono poi aggiunte le soluzioni di azo alle concentrazioni riportate in tabella.

Si versa poi in capsula di Petri e si lascia sotto cappa per favorire l’eliminazione del solvente.

 

Nel complesso film trasparente ed elastico.

 

Tabella dei film dati ad A. Porta

Matrice M1

A3

A5

PLA 4060D + TWEEN 80 al 10

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