title: Malonate-based inhibitors of mammalian serine racemase: kinetic characterization and structure-based computational study.
abstract: Overactivation of NMDA receptors has been implicated in various neuropathological conditions, including brain ischaemia, neurodegenerative disorders and epilepsy. Production of d-serine, an NMDA receptor co-agonist, from l-serine is catalyzed in vivo by the pyridoxal-5'-phosphate (PLP)-dependent enzyme serine racemase. Specific inhibition of this enzyme has been proposed as a promising strategy for treatment of neurological conditions caused by NMDA receptor dysfunction. Here we present the synthesis and activity analysis of a series of malonate-based inhibitors of mouse serine racemase (mSR). The compounds possessed IC50 values ranging from 40 ± 11 mM for 2,2-bis(hydroxymethyl)malonate down to 57 ± 1 μM for 2,2-dichloromalonate, the most effective competitive mSR inhibitor known to date. The structure-activity relationship of the whole series in the human orthologue (hSR) was interpreted using Glide docking, WaterMap analysis of hydration and quantum mechanical calculations based on the X-ray structure of the hSR/malonate complex. Docking into the hSR active site with three thermodynamically favourable water molecules was able to discern qualitatively between good and weak inhibitors. Further improvement in ranking was obtained using advanced PM6-D3H4X/COSMO semiempirical quantum mechanics-based scoring which distinguished between the compounds with IC50 better/worse than 2 mM. We have thus not only found a new potent hSR inhibitor but also worked out a computer-assisted protocol to rationalize the binding affinity which will thus aid in search for more effective SR inhibitors. Novel, potent hSR inhibitors may represent interesting research tools as well as drug candidates for treatment of diseases associated with NMDA receptor overactivation.
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Department of Biochemistry, Faculty of Natural Science, Charles University, Albertov 6, 128 43 Prague 2, Czech Republic.
authors.forename: Barbora
authors.initials: B
authors.lastname: Vorlová
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.
authors.forename: Dana
authors.initials: D
authors.lastname: Nachtigallová
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Department of Biochemistry, Faculty of Natural Science, Charles University, Albertov 6, 128 43 Prague 2, Czech Republic.
authors.forename: Jana
authors.initials: J
authors.lastname: Jirásková-Vaníčková
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46 Olomouc, Czech Republic.
authors.forename: Haresh
authors.initials: H
authors.lastname: Ajani
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.
authors.forename: Petr
authors.initials: P
authors.lastname: Jansa
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.
authors.forename: Jan
authors.initials: J
authors.lastname: Rezáč
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.
authors.forename: Jindřich
authors.initials: J
authors.lastname: Fanfrlík
authors.affiliation: Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46 Olomouc, Czech Republic.
authors.forename: Michal
authors.initials: M
authors.lastname: Otyepka
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46 Olomouc, Czech Republic.
authors.forename: Pavel
authors.initials: P
authors.lastname: Hobza
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Department of Biochemistry, Faculty of Natural Science, Charles University, Albertov 6, 128 43 Prague 2, Czech Republic. Electronic address: konval@uochb.cas.cz.
authors.forename: Jan
authors.initials: J
authors.lastname: Konvalinka
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic. Electronic address: lepsik@uochb.cas.cz.
authors.forename: Martin
authors.initials: M
authors.lastname: Lepšík
mesh_terms: D000818:Animals; D018360:Crystallography, X-Ray; D004305:Dose-Response Relationship, Drug; D004791:Enzyme Inhibitors / Q000138:chemical synthesis / Q000737:chemistry / Q000494:pharmacology*; D007700:Kinetics; D008314:Malonates / Q000138:chemical synthesis / Q000737:chemistry / Q000494:pharmacology*; D051379:Mice; D008958:Models, Molecular; D015394:Molecular Structure; D019998:Racemases and Epimerases / Q000037:antagonists & inhibitors* / Q000378:metabolism; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D000099300:Serine Racemase
chemical_list: D004791:Enzyme Inhibitors; D008314:Malonates; D019998:Racemases and Epimerases; D000099300:Serine Racemase; C030290:malonic acid
keywords: Docking; Human/mouse serine racemase; Malonate-based inhibitors; NMDA receptor; Pyridoxal-5′-phosphate-dependent enzyme; Semiempirical quantum mechanical calculations; Water thermodynamics