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Identification by virtual screening and in vitro testing of human DOPA decarboxylase inhibitors.

Daidone F, Montioli R, Paiardini A, Cellini B, Macchiarulo A, Giardina G, Bossa F, Borri Voltattorni C - PLoS ONE (2012)

Bottom Line: Co-administration of L-Dopa with peripheral DDC inhibitors (carbidopa or benserazide) is the most effective symptomatic treatment for PD.Although carbidopa and trihydroxybenzylhydrazine (the in vivo hydrolysis product of benserazide) are both powerful irreversible DDC inhibitors, they are not selective because they irreversibly bind to free PLP and PLP-enzymes, thus inducing diverse side effects.To our knowledge, a similar approach has not been reported yet in the field of DDC inhibitors discovery.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemical Sciences A Rossi Fanelli, University of Rome La Sapienza, Rome, Italy.

ABSTRACT
Dopa decarboxylase (DDC), a pyridoxal 5'-phosphate (PLP) enzyme responsible for the biosynthesis of dopamine and serotonin, is involved in Parkinson's disease (PD). PD is a neurodegenerative disease mainly due to a progressive loss of dopamine-producing cells in the midbrain. Co-administration of L-Dopa with peripheral DDC inhibitors (carbidopa or benserazide) is the most effective symptomatic treatment for PD. Although carbidopa and trihydroxybenzylhydrazine (the in vivo hydrolysis product of benserazide) are both powerful irreversible DDC inhibitors, they are not selective because they irreversibly bind to free PLP and PLP-enzymes, thus inducing diverse side effects. Therefore, the main goals of this study were (a) to use virtual screening to identify potential human DDC inhibitors and (b) to evaluate the reliability of our virtual-screening (VS) protocol by experimentally testing the "in vitro" activity of selected molecules. Starting from the crystal structure of the DDC-carbidopa complex, a new VS protocol, integrating pharmacophore searches and molecular docking, was developed. Analysis of 15 selected compounds, obtained by filtering the public ZINC database, yielded two molecules that bind to the active site of human DDC and behave as competitive inhibitors with K(i) values ≥10 µM. By performing in silico similarity search on the latter compounds followed by a substructure search using the core of the most active compound we identified several competitive inhibitors of human DDC with K(i) values in the low micromolar range, unable to bind free PLP, and predicted to not cross the blood-brain barrier. The most potent inhibitor with a K(i) value of 500 nM represents a new lead compound, targeting human DDC, that may be the basis for lead optimization in the development of new DDC inhibitors. To our knowledge, a similar approach has not been reported yet in the field of DDC inhibitors discovery.

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Core of compound 37.The core of compound 37 was used as a query (the Smiles annotation string used is shown in the text), using OpenBabel, to filter the Ambinter database. Positions where no substitutions were allowed during the search are coloured in red.
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pone-0031610-g007: Core of compound 37.The core of compound 37 was used as a query (the Smiles annotation string used is shown in the text), using OpenBabel, to filter the Ambinter database. Positions where no substitutions were allowed during the search are coloured in red.

Mentions: In order to identify molecules with increased activity and obtain insights into structure-activity relationships, we further expanded the class of active compounds resulting from the second VS by a substructure search carried out using the core of the most active compound 37 (Fig. 7). The OpenBabel substructure search tool (Open Babel v. 2.3.1, 2011) was used to filter the Ambinter database of small molecules, using as query the following SMILES notation (Weininger, 1988): [OH]c2[cH][cH]c(C = Nn1cnnc1)[cH]c2[OH]. Since the most potent compounds obtained in the second VS (see compounds 21, 37, 21) have a catechol ring with meta- and para- hydroxylic groups, the explicit hydrogens of the unsubstituted benzene carbon atoms and of the hydroxylic oxygen atoms were included in the SMILES notation in order to avoid the selection of compounds with substitution patterns involving these positions.


Identification by virtual screening and in vitro testing of human DOPA decarboxylase inhibitors.

Daidone F, Montioli R, Paiardini A, Cellini B, Macchiarulo A, Giardina G, Bossa F, Borri Voltattorni C - PLoS ONE (2012)

Core of compound 37.The core of compound 37 was used as a query (the Smiles annotation string used is shown in the text), using OpenBabel, to filter the Ambinter database. Positions where no substitutions were allowed during the search are coloured in red.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3285636&req=5

pone-0031610-g007: Core of compound 37.The core of compound 37 was used as a query (the Smiles annotation string used is shown in the text), using OpenBabel, to filter the Ambinter database. Positions where no substitutions were allowed during the search are coloured in red.
Mentions: In order to identify molecules with increased activity and obtain insights into structure-activity relationships, we further expanded the class of active compounds resulting from the second VS by a substructure search carried out using the core of the most active compound 37 (Fig. 7). The OpenBabel substructure search tool (Open Babel v. 2.3.1, 2011) was used to filter the Ambinter database of small molecules, using as query the following SMILES notation (Weininger, 1988): [OH]c2[cH][cH]c(C = Nn1cnnc1)[cH]c2[OH]. Since the most potent compounds obtained in the second VS (see compounds 21, 37, 21) have a catechol ring with meta- and para- hydroxylic groups, the explicit hydrogens of the unsubstituted benzene carbon atoms and of the hydroxylic oxygen atoms were included in the SMILES notation in order to avoid the selection of compounds with substitution patterns involving these positions.

Bottom Line: Co-administration of L-Dopa with peripheral DDC inhibitors (carbidopa or benserazide) is the most effective symptomatic treatment for PD.Although carbidopa and trihydroxybenzylhydrazine (the in vivo hydrolysis product of benserazide) are both powerful irreversible DDC inhibitors, they are not selective because they irreversibly bind to free PLP and PLP-enzymes, thus inducing diverse side effects.To our knowledge, a similar approach has not been reported yet in the field of DDC inhibitors discovery.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemical Sciences A Rossi Fanelli, University of Rome La Sapienza, Rome, Italy.

ABSTRACT
Dopa decarboxylase (DDC), a pyridoxal 5'-phosphate (PLP) enzyme responsible for the biosynthesis of dopamine and serotonin, is involved in Parkinson's disease (PD). PD is a neurodegenerative disease mainly due to a progressive loss of dopamine-producing cells in the midbrain. Co-administration of L-Dopa with peripheral DDC inhibitors (carbidopa or benserazide) is the most effective symptomatic treatment for PD. Although carbidopa and trihydroxybenzylhydrazine (the in vivo hydrolysis product of benserazide) are both powerful irreversible DDC inhibitors, they are not selective because they irreversibly bind to free PLP and PLP-enzymes, thus inducing diverse side effects. Therefore, the main goals of this study were (a) to use virtual screening to identify potential human DDC inhibitors and (b) to evaluate the reliability of our virtual-screening (VS) protocol by experimentally testing the "in vitro" activity of selected molecules. Starting from the crystal structure of the DDC-carbidopa complex, a new VS protocol, integrating pharmacophore searches and molecular docking, was developed. Analysis of 15 selected compounds, obtained by filtering the public ZINC database, yielded two molecules that bind to the active site of human DDC and behave as competitive inhibitors with K(i) values ≥10 µM. By performing in silico similarity search on the latter compounds followed by a substructure search using the core of the most active compound we identified several competitive inhibitors of human DDC with K(i) values in the low micromolar range, unable to bind free PLP, and predicted to not cross the blood-brain barrier. The most potent inhibitor with a K(i) value of 500 nM represents a new lead compound, targeting human DDC, that may be the basis for lead optimization in the development of new DDC inhibitors. To our knowledge, a similar approach has not been reported yet in the field of DDC inhibitors discovery.

Show MeSH
Related in: MedlinePlus