Identification of selective norbornane-type aspartate analogue inhibitors of the glutamate transporter 1 (GLT-1) from the chemical universe generated database (GDB).

A variety of conformationally constrained aspartate and glutamate analogues inhibit the glutamate transporter 1 (GLT-1, also known as EAAT2). To expand the search for such analogues, a virtual library of aliphatic aspartate and glutamate analogues was generated starting from the chemical universe database GDB-11, which contains 26.4 million possible molecules up to 11 atoms of C, N, O, F, resulting in 101026 aspartate analogues and 151285 glutamate analogues. Virtual screening was realized by high-throughput docking to the glutamate binding site of the glutamate transporter homologue from Pyrococcus horikoshii (PDB code: 1XFH ) using Autodock. Norbornane-type aspartate analogues were selected from the top-scoring virtual hits and synthesized. Testing and optimization led to the identification of (1R*,2R*,3S*,4R*,6R*)-2-amino-6-phenethyl-bicyclo[2.2.1]heptane-2,3-dicarboxylic acid as a new inhibitor of GLT-1 with IC(50) = 1.4 μM against GLT-1 and no inhibition of the related transporter EAAC1. The systematic diversification of known ligands by enumeration with help of GDB followed by virtual screening, synthesis, and testing as exemplified here provides a general strategy for drug discovery.

[1]  T. A. Connors,et al.  The pharmacology and tumour growth inhibitory activity of 1-aminocyclopentane-1-carboxylic acid and related compounds. , 1960, Biochemical pharmacology.

[2]  H. Mclennan,et al.  The synthesis and X-ray structures of the geometric isomers of 1-amino-1,2-cyclopentanedicarboxylic acid , 1993 .

[3]  A. Perosa,et al.  Hydroformylation of norbornene and 2,5-norbornadiene catalysed by platinum(0)-alkene complexes in the presence of methanesulfonic acid : determination of the stereochemistry of the reaction , 1993 .

[4]  J. Gasteiger,et al.  FROM ATOMS AND BONDS TO THREE-DIMENSIONAL ATOMIC COORDINATES : AUTOMATIC MODEL BUILDERS , 1993 .

[5]  N. Moss,et al.  Herpes simplex virus ribonucleotide reductase subunit association inhibitors: the effect and conformation of beta-alkylated aspartic acid derivatives. , 1994, Bioorganic & medicinal chemistry.

[6]  J. Wadiche,et al.  Functional comparisons of three glutamate transporter subtypes cloned from human motor cortex , 1994, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[7]  I. Izquierdo,et al.  Memory of inhibitory avoidance in the rat is regulated by glutamate metabotropic receptors in the hippocampus. , 1994, Behavioural pharmacology.

[8]  C. Cativiela,et al.  Study of the asymmetric diels-alder reaction of a chiral azlactone , 1994 .

[9]  C. Cativiela,et al.  Diastereoselective synthesis of (1S,2S,3R,4R) and (1R,2S,3R,4S)-bicyclo[2.2.1]hept-2-amino-2,3-dicarboxylic acids: New conformationally-constrained (S)-aspartic acid analogues , 1996 .

[10]  Gloria Rassu,et al.  Diastereoselective synthesis of , 1997 .

[11]  M. Kavanaugh,et al.  Structural determinants of substrates and inhibitors: probing glutamate transporters with 2,4-methanopyrrolidine-2,4-dicarboxylate. , 1998, Bioorganic & medicinal chemistry letters.

[12]  F. Fabris,et al.  DIASTEREOSELECTIVE CIS TO TRANS DESYMMETRIZATION OF DIMETHYL SUCCINATES , 1999 .

[13]  J. Dunlop,et al.  Inducible expression and pharmacology of the human excitatory amino acid transporter 2 subtype of L‐glutamate transporter , 1999, British journal of pharmacology.

[14]  M. Kavanaugh,et al.  Differentiation of substrate and nonsubstrate inhibitors of the high-affinity, sodium-dependent glutamate transporters. , 1999, Molecular pharmacology.

[15]  Y. Shigeri,et al.  Syntheses of optically pure beta-hydroxyaspartate derivatives as glutamate transporter blockers. , 2000, Bioorganic & medicinal chemistry letters.

[16]  P. V. van Rijen,et al.  Distribution of glutamate transporters in the hippocampus of patients with pharmaco-resistant temporal lobe epilepsy. , 2002, Brain : a journal of neurology.

[17]  M. Gobbi,et al.  Substrate inhibitors and blockers of excitatory amino acid transporters in the treatment of neurodegeneration: critical considerations. , 2003, European journal of pharmacology.

[18]  S. Amara,et al.  Characterization of novel L-threo-beta-benzyloxyaspartate derivatives, potent blockers of the glutamate transporters. , 2004, Molecular pharmacology.

[19]  J. Rothstein,et al.  Glutamate transporters: animal models to neurologic disease , 2004, Neurobiology of Disease.

[20]  E. Gouaux,et al.  Structure of a glutamate transporter homologue from Pyrococcus horikoshii , 2004, Nature.

[21]  M. Hediger,et al.  Identification of Mammalian Proline Transporter SIT1 (SLC6A20) with Characteristics of Classical System Imino* , 2005, Journal of Biological Chemistry.

[22]  M. Kavanaugh,et al.  The substituted aspartate analogue l-β-threo-benzyl-aspartate preferentially inhibits the neuronal excitatory amino acid transporter EAAT3 , 2005, Neuropharmacology.

[23]  Jean-Louis Reymond,et al.  Virtual exploration of the small-molecule chemical universe below 160 Daltons. , 2005, Angewandte Chemie.

[24]  R. Bridges,et al.  The excitatory amino acid transporters: pharmacological insights on substrate and inhibitor specificity of the EAAT subtypes. , 2005, Pharmacology & therapeutics.

[25]  Hwangseo Park,et al.  Critical assessment of the automated AutoDock as a new docking tool for virtual screening , 2006, Proteins.

[26]  J. Dunlop,et al.  Ligands targeting the excitatory amino acid transporters (EAATs). , 2006, Current topics in medicinal chemistry.

[27]  T. Gefflaut,et al.  Stereoselective chemoenzymatic synthesis of the four stereoisomers of l-2-(2-carboxycyclobutyl)glycine and pharmacological characterization at human excitatory amino acid transporter subtypes 1, 2, and 3. , 2006, Journal of medicinal chemistry.

[28]  P. Peluso,et al.  Rhodium catalyzed hydroformylation of 2-phenylsulfonylbicyclo[2.2.1] alkenes: effect of the phenylsulfonyl group , 2006 .

[29]  R. D. O'Shea,et al.  Transporters for L‐glutamate: An update on their molecular pharmacology and pathological involvement , 2007, British journal of pharmacology.

[30]  T. Ueda,et al.  The Glutamate Uptake System in Presynaptic Vesicles: Further Characterization of Structural Requirements for Inhibitors and Substrates , 2008, Neurochemical Research.

[31]  Jean-Louis Reymond,et al.  Virtual Exploration of the Chemical Universe up to 11 Atoms of C, N, O, F: Assembly of 26.4 Million Structures (110.9 Million Stereoisomers) and Analysis for New Ring Systems, Stereochemistry, Physicochemical Properties, Compound Classes, and Drug Discovery , 2007, J. Chem. Inf. Model..

[32]  Eric Gouaux,et al.  Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter , 2007, Nature.

[33]  D. Bertrand,et al.  Discovery of NMDA Glycine Site Inhibitors from the Chemical Universe Database GDB , 2008, ChemMedChem.

[34]  Lorenz C. Blum,et al.  970 million druglike small molecules for virtual screening in the chemical universe database GDB-13. , 2009, Journal of the American Chemical Society.

[35]  Jean-Louis Reymond,et al.  3-(aminomethyl)piperazine-2,5-dione as a novel NMDA glycine site inhibitor from the chemical universe database GDB. , 2009, Bioorganic & medicinal chemistry letters.

[36]  Lorenz C. Blum,et al.  Chemical space as a source for new drugs , 2010 .

[37]  D. Bertrand,et al.  Exploring α7-Nicotinic Receptor Ligand Diversity by Scaffold Enumeration from the Chemical Universe Database GDB. , 2010, ACS medicinal chemistry letters.