Sandbox Reserved 957: Difference between revisions
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Catalytic domain is conserved for the PDE family, between 20% and 40%, and the variant reactions of the PDE inhibitors on the different PDEs may be caused by the more variant regulatory sites [25].<br \> | Catalytic domain is conserved for the PDE family, between 20% and 40%, and the variant reactions of the PDE inhibitors on the different PDEs may be caused by the more variant regulatory sites [25].<br \> | ||
The catalytic domain has 3 helical subdomains [24]:<br \> | The catalytic domain has 3 helical subdomains [24]:<br \> | ||
* A N-terminal cyclin-fold region with eight helixes [26]: 5 α-helixes (1, 3, 5, 6 and 8) and 3 310-helixes (2,4, and 7), from the 537th to the 678th residues.<br \> | |||
* A linker domain: two antiparallels α9 and α10 helixes, and between a disordered region, from the 679th to the 725th residues.<br \> | |||
* A C-terminal buddle pocket with eight helixes: 5 long α-helixes (11, 12, 14, 17 and 18) and 3 smaller helixes (13, 15 and 16), from the 726th to the 860th residues.<br \> | |||
** α5, 6 and 8 surround α3 and form an interface with the linker domain and the CTD.<br \> | |||
The catalytic site is a pocket which is 330Å in volume and a deep of 10Å, with a narrow entry. There are 4 regions: M (with 2 metallic ions), H (hydrophobic), Q (for the substrate), L (the lid or “H-Loop” on both N-term and linker domain). M site is surrounded by the helixes α6, 8, 9, 10 and 12. A majority of aliphatic or hydrophobic residues, that creates the hydrophobic pocket [2].<br \> | The catalytic site is a pocket which is 330Å in volume and a deep of 10Å, with a narrow entry. There are 4 regions: M (with 2 metallic ions), H (hydrophobic), Q (for the substrate), L (the lid or “H-Loop” on both N-term and linker domain). M site is surrounded by the helixes α6, 8, 9, 10 and 12. A majority of aliphatic or hydrophobic residues, that creates the hydrophobic pocket [2].<br \> | ||
M site contains:<br \> | M site contains:<br \> | ||
* The Me-1 and Me-2 sites are occupied by metal ions, Zinc within Me-1 and within Me-2, Zinc, Magnesium or Manganese [5],<br \> | |||
* The residues His617, Asp654, Asp764, His653 and two H2O (W1 et W2) binding zinc:<br \> | |||
** The crucial Asp764 [3] and the conserved His617 and 653[4], which bind one Zinc ion, are fundamental for the catalytic activity.<br \> | |||
** Zinc is critical for catalytic activity, but it isn't implied in the formation of the hydrophobic pocket. In fact, even if the His617and 653 are lost and so the Zn not bound, a massive addition of Manganese[4] in the medium allows a reactivation of catalysis.<br \> | |||
* W2 binds Zn and Mg [24],<br \> | |||
* And there are 3 hydrogen bonds between 3 H2O and the conserved resides His657, Asp682 and His685 [24].<br \> | |||
Q site contains:<br \> | Q site contains:<br \> | ||
* In particular the conserved residues Gln817, Phe820, Val782 and Tyr612. [24]<br \> | |||
* The hydrogen bonds, between Gln817 and 775, Gln775 and Ala767, Gln775 and Trp853, imply an interaction between Gln817 and the cGMP purine. Thus, it improves the specificity for the cGMP, against cAMP. [24]<br \> | |||
* And Tyr612, Val782, Leu785 an Phe820 bind the cGMP through this pyrazol ring and π-π interactions between Gln817 and the phenyl ring. [24]<br \> | |||
** So, the conserved hydrophobic residue Tyr 612 is critical in the maintaining of the affinity. [3]<br \> | |||
H site:<br \> | H site:<br \> | ||
* In particular the residues Phe786, Ala783, Leu804, Val782. [24]<br \> | |||
L site:<br \> | L site:<br \> | ||
* In particular the hydrophobic residues Tyr664, Met816, Ala823, Gly819. [24]<br \> | |||
Besides, the kcat of the catalytic fragment decreases 40-fold and 8-fold if the residues His603 and Asp644 are mutated, and so there are important in the catalytic activity [5,3]. Two others residues are significant: the Gln778 which is important for cGMP affinity but have no impact on cAMP affinity H-loop [8] and the conserved Gly659 which is important for substrate affinity and catalytic activity because it determinates H-loop conformation [21] (see below).<br \> | Besides, the kcat of the catalytic fragment decreases 40-fold and 8-fold if the residues His603 and Asp644 are mutated, and so there are important in the catalytic activity [5,3]. Two others residues are significant: the Gln778 which is important for cGMP affinity but have no impact on cAMP affinity H-loop [8] and the conserved Gly659 which is important for substrate affinity and catalytic activity because it determinates H-loop conformation [21] (see below).<br \> | ||
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In the treatment erection dysfunction, the inhibitors Sildenafil, Vardenafil and Tadalafil are used, like in the pulmonary hypertension[6]. Sildenafil may cure sleeping trouble after a intercontinental travel [11], may help to recover neural liaisons after an injury (the motor function[12] and the sensory motor function[13]) and can be vascular effects.<br \> | In the treatment erection dysfunction, the inhibitors Sildenafil, Vardenafil and Tadalafil are used, like in the pulmonary hypertension[6]. Sildenafil may cure sleeping trouble after a intercontinental travel [11], may help to recover neural liaisons after an injury (the motor function[12] and the sensory motor function[13]) and can be vascular effects.<br \> | ||
* PDE5 inhibitors might help physical condition in Duchene muscular dystrophy[14], improve of cognitive function [9]and have antidepressant effect[10] , also they might have an artero[15] and endothelial cell protective effect[16] so they have cardiac protection effect[17] (controversial, cf. clinical trial “RELAX”), finally they slow tumer cell growth (Tadalafil-like)[18]<br \> | |||
* There are other PDE5 inhibitors: IBMX, Icarisid II and Udenafil.<br \> | |||
* No interaction between the M site and the inhibitors<br \> | |||
For the Sildenafil:<br \> | For the Sildenafil:<br \> | ||
* 3 parts (R1: pyrazolopyrimidinone group; R2: ethoxyphenyl; R3: methylpiperazine)<br \> | |||
* It is bound near Metallic ions but does not interact with them.<br \> | |||
Binding amino acid for the Sildenafil:<br \> | Binding amino acid for the Sildenafil:<br \> | ||
* R1 group have contacts with Gln817 (2 hydrogen bounds, so it increases Sildenafil affinity), Phe820 (Sildenafil stacks against it), Try612 (hydrogen bound so it increases Sildenafil affinity [24]), Leu765 and Ala767 [21]. And there is hydrophobic interactions between the pyrazol ring and residues Val782, Leu785, Tyr612 and Phe820 [24].<br \> | |||
* R2 group is in the H pocket and has Van der Waals bounds with Val 782, Ala 783, Phe 786, Leu 804, Ile 813, Gln 817, Phe801. And interaction Pi-Pi between the phenyl ring and the Phe820.<br \> | |||
* R3 group is in the L pocket and has contacts with Asn 662, Ser 663, Tyr 664, Ile 665 (in the H-loop), Leu 804, Phe 801 | |||
* Gly659 is modified by Sildenafil presence in PDE5, ϕ and φ angles are increased (from 76-105° to 104-109° for ϕ and from 3-22° to 139-141° for φ) and ω angle is not changed. [21]<br \> | |||
H-loop:<br \> | H-loop:<br \> | ||
For each inhibitor, H-loop take a different and originally (comparatively to other PDEs) tertiary structure (and there are also minor modifications of the N-loop (788-811) ):<br \> | For each inhibitor, H-loop take a different and originally (comparatively to other PDEs) tertiary structure (and there are also minor modifications of the N-loop (788-811) ):<br \> | ||
* For an unliganded PDE5, H-loop take a coil conformation. [21]<br \> | |||
* In case of Sildenafil binding, a turn and an 310 helix (from 672 to 675) appear, and residues from 668 to 676 are disordered. The all loop cover the active site (by migrate of 24 Å from unliganded PDE5 loop structure, so the active site become a closed pocket). [21]<br \> | |||
* H-loop is less important in the interactions for Sildenafil and Icarisid II than cGMP.<br \> | |||
== Regulation == | == Regulation == | ||