Inhibition of Human Serine Racemase, an Emerging Target for Medicinal Chemistry

Abstract

Proteins of glutamatergic NMDA receptor signaling pathways have been studied as targets for intervention in a variety of neuropathological conditions, including neurodegenerations, epilepsy, neuropathic pain, drug addiction, and schizophrenia. High activity NMDA-blocking agents have been designed to treat some of these disorders; however, their effect is often compromised by undesirable side effects. Therefore, alternative ways of modulating NMDA receptor function need to be sought after. The opening of the NMDA receptor ion channel requires occupation of two distinct binding sites, the glutamate site and the glycine site. It has been shown that D-serine, rather than glycine, can trigger the physiological NMDA receptor function. D-serine is a product of the activity of a specific enzyme, serine racemase (SR), which was identified a decade ago. SR has therefore emerged as a new potential target for the NMDA-receptor-based diseases. There is evidence linking increased levels of D-Ser to amyotrophic lateral sclerosis and Alzheimer's disease and decreased concentrations of D-serine to schizophrenia. SR is a pyridoxal-5'-phosphate dependent enzyme found in the cytosol of glial and neuronal cells. It is activated by ATP, divalent cations like Mg(2+) or Ca(2+), and reducing agents. This paper reviews the present literature on the activity and inhibition of mammalian SRs. It summarizes approaches that have been applied to design SR inhibitors and lists the known active compounds. Based on biochemical and docking analyses, i) we delineate for the first time the ATP binding site of human SR, and ii) we suggest possible mechanisms of action for the active compounds. In the end, we discuss the SR features that make the discovery of its inhibitors a challenging, yet very important, task of medicinal chemistry.

Cyclopropane derivatives as potential human serine racemase inhibitors: unveiling novel insights into a difficult target

“…For instance, the addition of a single methyl group to malonate has a detrimental effect on the 25 activity, giving a compound with 30-fold decreased activity 25 , despite an almost perfect docking into the binding site. To compare our results with those previously published and to prove the detrimental effects of hydrophobic contributions for SR inhibitors, we purchased and tested cinnamic acid, that was reported to act as a moderate SR inhibitor 23 , with an affinity for the enzyme higher than that of L-serine. Not surprisingly, it turned out to be completely inactive under our test conditions.…”

“…We prepared and tested as potential SR inhibitors the cyclopropane derivatives reported in Table 1. Compound 4 was synthesized on the basis of the similarity with malonate and compound 5, trans 1,2-cyclopropanedicarboxylic acid, was synthesized to probe the effect of a trans-configuration of the two carboxylate moieties, also on the basis of the mild inhibition observed for fumaric acid 23 . With compounds 6 and 7, we aimed at exploring the effect of the esterification of one of the two carboxylate moieties, while with 8 we explored the effect of a further functionalization of the cyclopropane ring.…”

“…With compounds 6 and 7, we aimed at exploring the effect of the esterification of one of the two carboxylate moieties, while with 8 we explored the effect of a further functionalization of the cyclopropane ring. Finally, compound 9 was purchased from Sigma-Aldrich (St. Louis, MO) as a constrained analogue of cinnamic acid, previously reported to be a fairly good inhibitor of SR 23 . The six compounds were assayed in vitro on recombinant human SR. To our surprise, all the cyclopropane derivatives resulted to be much less potent than malonate.…”

“…Crystal structures of eukaryotic SR were solved from different sources, human, rat 20 and Schizosaccharomyces Pombe 21,22 , in holo form or in complex with the inhibitor malonate ( Figure 1). Despite the availability of structural data and the identification of a few inhibitors [23][24][25][26] , the development of specific and more potent SR inhibitors remains very challenging 13 . While this work was in preparation, three papers aiming at the identification of novel SR inhibitors were published.…”

“…designed substrate analogues as potential inhibitors, Vorlova et al 25 synthesized a series of malonate analogues, and Mori et al 24 identified novel potential inhibitors of SR by in silico ligand-based screening. All the compounds reported in these works exhibit very low inhibitory potencies, with inhibition constants in the high micromolar to millimolar range, with the only exception of 2,2-dichloromalonate, characterized by a K i of 57 lM (Figure 1 Inspired by SR inhibitors based on the structure of malonate 23 , we investigated the possibility of developing a new series of potential SR inhibitors based on the cyclopropane scaffold. The rationale for our choice was the overall similarity between cis 1,2-cyclopropanedicarboxylic acid and malonic acid.…”