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Molecular Mechanism Underlying the Action of Substituted Pro-Gly Dipeptide Noopept.

Vakhitova YV, Sadovnikov SV, Borisevich SS, Ostrovskaya RU, A Gudasheva T, Seredenin SB - Acta Naturae (2016 Jan-Mar)

Bottom Line: Piracetam (1 mM) failed to affect significantly any of the TF under study.The results of molecular docking showed that Noopept (L-isomer), as well as its metabolite, L-isomer of N-phenyl-acetylprolyl, unlike its pharmacologically ineffective D-isomer, is able to bind to the active site of prolyl hydroxylase 2.The obtained data allow one to propose the HIF-positive effect as the primary mechanism of the activity of this Pro-Gly-containing dipeptide.

View Article: PubMed Central - PubMed

Affiliation: State Zakusov Institute of Pharmacology , Baltiyskaya Str., 8, 125315, Moscow, Russia ; Institute of Biochemistry and Genetics of Ufa Scientific Centre RAS, Prospekt Oktyabrya, 71, 450065 , Ufa, Russia.

ABSTRACT
This study was performed in order to reveal the effect of Noopept (ethyl ester of N-phenylacetyl-Lprolylglycine, GVS-111) on the DNA-binding activity of transcriptional factors (TF) in HEK293 cells transiently transfected with luciferase reporter constructs containing sequences for CREB, NFAT, NF-κB, p53, STAT1, GAS, VDR, HSF1, and HIF-1. Noopept (10 μM) was shown to increase the DNA-binding activity of HIF-1 only, while lacking the ability to affect that of CREB, NFAT, NF-κB, p53, STAT1, GAS, VDR, and HSF1. Noopept provoked an additional increase in the DNA-binding activity of HIF-1 when applied in conditions of CoCl2-induced HIF- 1 stabilization. The degree of this HIF-positive effect of Noopept was shown to be concentration-dependent. Piracetam (1 mM) failed to affect significantly any of the TF under study. The results of molecular docking showed that Noopept (L-isomer), as well as its metabolite, L-isomer of N-phenyl-acetylprolyl, unlike its pharmacologically ineffective D-isomer, is able to bind to the active site of prolyl hydroxylase 2. Taking into account the important role of the genes activated by HIF-1 in the formation of an adaptive response to hypoxia, data on the ability of Noopept to provoke a selective increase in the DNA-binding activity of HIF-1 explain the wide spectrum of neurochemical and pharmacological effects of Noopept revealed before. The obtained data allow one to propose the HIF-positive effect as the primary mechanism of the activity of this Pro-Gly-containing dipeptide.

No MeSH data available.


Related in: MedlinePlus

Analysis of the active site of prolyl hydroxylase enzyme 2. A– active center occupied by “native” ligand.B – interaction between inhibitor and amino acid residues of theenzyme (docking solution)
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Figure 1: Analysis of the active site of prolyl hydroxylase enzyme 2. A– active center occupied by “native” ligand.B – interaction between inhibitor and amino acid residues of theenzyme (docking solution)

Mentions: The surrounding area of the native inhibitor (ZINC: 24800213) with adjacentamino acid residues is 6.5 A and contains Arg383, Tyr310, Tyr303 andFe2+. Analysis of the 2G19 enzyme active center showed that Arg383and Tyr329 form hydrogen bonds with the carboxyl group of the ZINC 24800213native inhibitor; Tyr310 and Tyr303 form a π–π electroninteraction with the aromatic rings of the ligand. The amino acid residuesTrp389, Trp258, Met299, and Ile256 form a hydrophobic pocket(Fig. 1).All water molecules were removed from the active center duringpreparation of the enzyme structure for the docking procedure. Re-docking ofthe native ligand into the PHD2 enzyme active site accurately reproduces themode of binding between the ligand and enzyme that has been determinedcrystallographically. The root-mean-square deviation is 0.44 A. The subprogramFlexX [21] allows to perform theprocedure of ligand docking(Table) andestimate the energy of binding between the ligand and receptor in the active site.The number of docking decisions can be large enough, and the choice of an optimalsolution is based on the minimum value of the binding energy in combination with aminimum root-mean-square deviation (RMSD) value when the ligand is in the bindingsite. Next, the selected position is subjected to further calculation: assessment ofthe affinity energy between the ligand and binding site(ΔGHYDE, kJ/mol) and evaluation of ligand effectiveness[22, 23].A detailed algorithm of the calculation is described in[22]. It is noted that it is optimal touse two successive stages of the selection of the leader compound among theligands.


Molecular Mechanism Underlying the Action of Substituted Pro-Gly Dipeptide Noopept.

Vakhitova YV, Sadovnikov SV, Borisevich SS, Ostrovskaya RU, A Gudasheva T, Seredenin SB - Acta Naturae (2016 Jan-Mar)

Analysis of the active site of prolyl hydroxylase enzyme 2. A– active center occupied by “native” ligand.B – interaction between inhibitor and amino acid residues of theenzyme (docking solution)
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4837574&req=5

Figure 1: Analysis of the active site of prolyl hydroxylase enzyme 2. A– active center occupied by “native” ligand.B – interaction between inhibitor and amino acid residues of theenzyme (docking solution)
Mentions: The surrounding area of the native inhibitor (ZINC: 24800213) with adjacentamino acid residues is 6.5 A and contains Arg383, Tyr310, Tyr303 andFe2+. Analysis of the 2G19 enzyme active center showed that Arg383and Tyr329 form hydrogen bonds with the carboxyl group of the ZINC 24800213native inhibitor; Tyr310 and Tyr303 form a π–π electroninteraction with the aromatic rings of the ligand. The amino acid residuesTrp389, Trp258, Met299, and Ile256 form a hydrophobic pocket(Fig. 1).All water molecules were removed from the active center duringpreparation of the enzyme structure for the docking procedure. Re-docking ofthe native ligand into the PHD2 enzyme active site accurately reproduces themode of binding between the ligand and enzyme that has been determinedcrystallographically. The root-mean-square deviation is 0.44 A. The subprogramFlexX [21] allows to perform theprocedure of ligand docking(Table) andestimate the energy of binding between the ligand and receptor in the active site.The number of docking decisions can be large enough, and the choice of an optimalsolution is based on the minimum value of the binding energy in combination with aminimum root-mean-square deviation (RMSD) value when the ligand is in the bindingsite. Next, the selected position is subjected to further calculation: assessment ofthe affinity energy between the ligand and binding site(ΔGHYDE, kJ/mol) and evaluation of ligand effectiveness[22, 23].A detailed algorithm of the calculation is described in[22]. It is noted that it is optimal touse two successive stages of the selection of the leader compound among theligands.

Bottom Line: Piracetam (1 mM) failed to affect significantly any of the TF under study.The results of molecular docking showed that Noopept (L-isomer), as well as its metabolite, L-isomer of N-phenyl-acetylprolyl, unlike its pharmacologically ineffective D-isomer, is able to bind to the active site of prolyl hydroxylase 2.The obtained data allow one to propose the HIF-positive effect as the primary mechanism of the activity of this Pro-Gly-containing dipeptide.

View Article: PubMed Central - PubMed

Affiliation: State Zakusov Institute of Pharmacology , Baltiyskaya Str., 8, 125315, Moscow, Russia ; Institute of Biochemistry and Genetics of Ufa Scientific Centre RAS, Prospekt Oktyabrya, 71, 450065 , Ufa, Russia.

ABSTRACT
This study was performed in order to reveal the effect of Noopept (ethyl ester of N-phenylacetyl-Lprolylglycine, GVS-111) on the DNA-binding activity of transcriptional factors (TF) in HEK293 cells transiently transfected with luciferase reporter constructs containing sequences for CREB, NFAT, NF-κB, p53, STAT1, GAS, VDR, HSF1, and HIF-1. Noopept (10 μM) was shown to increase the DNA-binding activity of HIF-1 only, while lacking the ability to affect that of CREB, NFAT, NF-κB, p53, STAT1, GAS, VDR, and HSF1. Noopept provoked an additional increase in the DNA-binding activity of HIF-1 when applied in conditions of CoCl2-induced HIF- 1 stabilization. The degree of this HIF-positive effect of Noopept was shown to be concentration-dependent. Piracetam (1 mM) failed to affect significantly any of the TF under study. The results of molecular docking showed that Noopept (L-isomer), as well as its metabolite, L-isomer of N-phenyl-acetylprolyl, unlike its pharmacologically ineffective D-isomer, is able to bind to the active site of prolyl hydroxylase 2. Taking into account the important role of the genes activated by HIF-1 in the formation of an adaptive response to hypoxia, data on the ability of Noopept to provoke a selective increase in the DNA-binding activity of HIF-1 explain the wide spectrum of neurochemical and pharmacological effects of Noopept revealed before. The obtained data allow one to propose the HIF-positive effect as the primary mechanism of the activity of this Pro-Gly-containing dipeptide.

No MeSH data available.


Related in: MedlinePlus