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Analysis of molecular interaction fields based on the published crystal structure of thapsigargin bound to the sarco/endoplasmatic reticulum Ca²⁺-ATPase and analysis of the volume and shape of the ligand binding site and of the SERCA−thapsigargin interactions have enabled design of two new compounds inhibiting SERCA in the subpicomolar range. The two inhibitors were synthesized using (S)-carvone as starting material and found to be 3 and 10 times more potent than thapsigargin.

We have previously described a series of competitive GABAA antagonists derived from the low-efficacy partial agonist 5-(4-piperidyl)-3-isoxazolol (4-PIOL, 4). The 2-naphthylmethyl analogue, 4-(2-naphthylmethyl)-5-(4-piperidyl)-3-isoxazolol (5), provided affinity for the GABAA receptor site higher than that of the standard GABAA receptor antagonist, SR 95531 (3). Molecular modeling studies of these compounds exposed a cavity at the receptor recognition site capable of accommodating aromatic groups of substantial size in the 4-position in the 3-isoxazolol ring. Here we present a series of analogues of 5, with various substituents in different positions in the naphthyl ring system (6a−k), and compounds with aromatic substituents directly attached to the 4-position of the 3-isoxazolol ring (7l−n). The compounds have been pharmacologically characterized using receptor-binding assays and electrophysiological whole-cell patch-clamp techniques. All of the tested compounds show affinity for the GABAA receptor site. While the 5-, 7-, and 8-bromo analogues, 6b−d, showed receptor affinities (Ki = 45, 109, and 80 nM, respectively) comparable with that of 5 (Ki = 49 nM), the 1-bromo analogue, 6a, provided the highest receptor affinity of the series (Ki = 10 nM). Introduction of a series of different substituents in the 1-position in the 2-naphthyl ring system led to compounds, 6e−k, with retained high affinity for the GABAA receptor (Ki = 16−250 nM). Introduction of a phenyl ring directly into the 4-position on the 3-isoxazolol ring gave a 41-fold increase in affinity relative to that of 4-PIOL. In whole-cell patch-clamp recordings from cultured cerebral cortical neurons, all of the tested compounds were able to inhibit the effect of the specific GABAA agonist isoguvacine, 6a showing antagonist potency (IC50 = 42 nM) markedly higher than that of 3 (IC50 = 240 nM). Molecular modeling studies, based on the compounds described, emphasized the importance of the distal ring in 5 for receptor affinity and the considerable dimensions of the proposed receptor cavity. Furthermore, the phenyl rings in 7l and in 6k were shown to represent highly favorable positions for an aromatic ring in previously unexplored receptor regions in terms of a pharmacophore model.

On the basis of structural studies, chloro-homoibotenic acid (Cl-HIBO) was designed and synthesized. Cl-HIBO was characterized in binding and electrophysiology experiments on native and cloned subtypes of GluRs. Electrophysiological selectivities ranged from 275 to 1600 for GluR1/2 over GluR3/4. The potent AMPA receptor activity was strongly desensitizing and the neurotoxicity similar to AMPA. Thus, Cl-HIBO is the most subtype selective agonist reported to date on GluR1/2, and offers a new standard for selectively studying subtypes of AMPA receptors.

A new class of 5-heteroaryl-substituted 1-(4-fluorophenyl)-3-(4-piperidinyl)-1H-indoles as highly selective and potentially CNS-active α1-adrenoceptor antagonists is described. The compounds are derived from the antipsychotic sertindole. The structure−affinity relationships of the 5-heteroaryl substituents, and the substituents on the piperidine nitrogen atom were optimized with respect to affinity for α1 adrenoceptors and selectivity in respect to dopamine (D1-4) and serotonin (5-HT1A-1B and 5-HT2A,2C) receptors. The most selective compound obtained, 3-{4-[1-(4-fluorophenyl)-5-(1-methyl-1,2,4-triazol-3-yl)-1H-indol-3-yl]-1-piperidinyl}propionitrile (15c), has affinities of 0.99, 3.2, and 9.0 nM for the α1a, α1b, and α1d adrenoceptor subtypes, respectively, and a selectivity for adrenergic α1a receptors in respect to dopamine D2, D3, and D4 and serotonin 5-HT2A and 5-HT2C higher than 900, comparable to the selectivity of prazosin. In addition, the compound is more than 150-fold selective in respect to serotonin 5-HT1A and 5-HT1B receptors. A new basic pharmacophore for α1-adrenoceptor antagonists based on a previously reported pharmacophore model for dopamine D2 antagonist is suggested.

Ionotropic glutamate receptors (iGluRs) constitute a family of ligand-gated ion channels that are essential for mediating fast synaptic transmission in the central nervous system. This study presents a high-resolution X-ray structure of the competitive antagonist (S)-2-amino-3-[5-tert-butyl-3-(phosphonomethoxy)-4-isoxazolyl]propionic acid (ATPO) in complex with the ligand-binding core of the receptor. Comparison with the only previous structure of the ligand-binding core in complex with an antagonist, 6,7-dinitro-2,3-quinoxalinedione (DNQX) (Armstrong, N.; Gouaux, E. Neuron 2000, 28, 165−181), reveals that ATPO and DNQX stabilize an open form of the ligand-binding core by different sets of interactions. Computational techniques are used to quantify the differences between these two ligands and to map the binding site. The isoxazole moiety of ATPO acts primarily as a spacer, and other scaffolds could potentially be used. Whereas agonists induce substantial domain closures compared to the apo structure, ATPO only induces minor conformational changes. These results are consistent with the hypothesis that domain closure is related to receptor activation. To facilitate the design of novel AMPA receptor antagonists, we present a modified model of the binding site that includes key residues involved in ligand recognition.

To further develop and evaluate a pharmacophore model previously proposed by Cook and co-workers (Drug Des. Discovery 1995, 12, 193−248) for ligands binding to the benzodiazepine site of the GABAA receptor, 40 new flavone derivatives have been synthesized and their affinities for the benzodiazepine site have been determined. Two new regions of steric repulsive interactions between ligand and receptor have been characterized, and the receptor region in the vicinity of 6- and 3‘-substituents has been mapped out. 2‘-Hydroxy substitution is shown to give a significant increase in affinity, which is interpreted in terms of a novel hydrogen bond interaction with the previously proposed hydrogen bond-accepting site A2. On the basis of the results of these studies and the refined pharmacophore model, 5‘-bromo-2‘-hydroxy-6-methylflavone, the highest affinity flavone derivative reported so far (Ki = 0.9 nM), was successfully designed. A comparison of the pharmacophore model with a recently proposed alternative model (Marder; et al. Bioorg. Med. Chem., 2001, 9, 323−335) has been made.

A number of analogues of the low-efficacy partial GABAA agonist 5-(4-piperidyl)-3-isoxazolol (4-PIOL, 5), in which the 4-position of the 3-isoxazolol ring was substituted by different groups, were synthesized and tested as GABAA receptor ligands. Substituents of different size and structural flexibility such as alkyl, phenylalkyl, diphenylalkyl, and naphthylalkyl were explored. Pharmacological characterization of the synthesized compounds was carried out using receptor binding assays and by electrophysiological experiments using whole-cell patch-clamp techniques. Whereas none of these compounds significantly affected GABAB receptor sites or GABA uptake, they did show affinity for the GABAA receptor site. While alkyl or benzyl substitution, compounds 7a−h, provided receptor affinities comparable with that of 5 (Ki = 9.1 μM), diphenylalkyl and naphthylalkyl substitution, as in compounds 7m−t, resulted in a dramatic increase in affinity relative to 5. The 3,3-diphenylpropyl and the 2-naphthylmethyl analogues, compounds 7s and 7m, respectively, showed the highest affinities of the series (Ki = 0.074 μM and Ki = 0.049 μM). In whole-cell patch-clamp recordings from cultured cerebral cortical neurons, all of the tested compounds were able to inhibit the effect of the specific GABAA agonist isoguvacine (1), compounds 7m and 7s showing antagonist potency (IC50 = 0.37 μM and IC50 = 0.02 μM) comparable with or markedly higher than that of the standard GABAA antagonist 4 (IC50 = 0.24 μM). Highly potent convulsant activity was demonstrated in mice with compounds 7m (ED50 = 0.024 μmol/kg) and 7s (ED50 = 0.21 μmol/kg) after intracerebroventricular administration, whereas no effects were found after subcutaneous administration. According to a previously proposed pharmacophore model for GABAA receptor agonists, a receptor cavity in the vicinity of the 4-position of the 3-isoxazolol ring in 4-PIOL exists. A molecular modeling study, based on compounds 7o,m,l,q,s, was performed to explore the dimensions and other properties of the receptor cavity. This study demonstrates the importance of the arylalkyl substituents in 7m and 7s and the considerable dimensions of this proposed receptor cavity.

(S)-CPW399 (2b) is a novel, potent, and subtype-selective AMPA receptor full agonist that, unlike (S)-willardiine and related compounds, in mouse cerebellar granule cells, stimulated an increase in [Ca²⁺]i, and induced neuronal cell death in a time- and concentration-dependent manner. Compound 2b appears to be a weakly desensitizing, full agonist at AMPA receptors and therefore represents a new pharmacological tool to investigate the role of AMPA receptors in excitotoxicity and their molecular mechanisms of desensitization.

In this study, the first density functional theory calculations on B12 models that contain the entire corrin ring are presented to evaluate earlier findings by other groups. Eight octahedral corrin systems with various axial ligands have been subject to a full density functional theory (DFT) lacvp** geometry optimization in vacuo. The largest of these calculations included around 1000 basis functions. For energies of optimized structures, we increased the basis set to a triple-ζ valence type. The effects of the different axial substituents on the crucial Co−C bond length and the corrin folding have been evaluated. We find a systematic cis-steric effect and a less systematic trans induction. The corrin framework is fairly inert toward the size of the axial R-ligands, which argues against a mechanochemical trigger mechanism. The HOMO−LUMO gap increases through the steric series via a lowering of the HOMO energy, making the corrins less susceptible to homolytic cleavage. Rather different equilibrium structures of adenosylcobalamin and methylcobalamin models are anticipated from this study, which also indicates that the former has ca. 5 kcal/mol higher HOMO and LUMO energy. This is a theoretical explanation why adenosylcobalamin is more easily homolyzed, whereas methylcobalamin is heterolyzed.

In the past few years the focus on central acetylcholine receptors has shifted from compounds with affinity for muscarinic acetylcholine receptors (mAChR) to compounds with affinity for nicotinic acetylcholine receptors (nAChR). The therapeutic potential includes treatment of a variety of diseases, e.g., Alzheimer's disease, Parkinson's disease, and Tourette's syndrome. This work describes the synthesis of six novel series of potent ligands with nanomolar affinity for the α4β2 nAChR subtype. Structure−activity relationship (SAR) was evaluated by the calculation of a 3D-QSAR model. 3D-QSAR analysis of the compounds using the GRID/GOLPE methodology resulted in a model of high quality (R² = 0.97, Q² = 0.81). The coefficient plots reveal that the steric interactions between the target and our compounds are of major importance for the affinity. Bulky substituents in the 6-position of the pyridine ring will reduce the affinity of the compounds, whereas bulky ring systems including a sp³-nitrogen will increase the affinity of the compounds.

The affinities for the benzodiazepine binding site of the GABAA receptor of 21 flavonoids have been studied using [³H]flumazenil binding to rat cortical membranes in vitro. We show that flavonoids with high affinity for the benzodiazepine receptor in vitro spanning the whole efficacy range from agonists (1q) to inverse agonists (1l) can be synthesized. The receptor binding properties of the flavonoids studied can successfully be rationalized in terms of a comprehensive pharmacophore model recently developed by Cook and co-workers (Drug Des. Dev. 1995, 12, 193−248), supporting the validity of this model. However, in contrast to the requirement by the model that an interaction with the hydrogen bond-accepting site A2 is necessary for compounds to display inverse agonistic activity, 6-methyl-3‘-nitroflavone (1l), which cannot engage in such an interaction, nevertheless displays inverse agonism. The analysis of the binding affinities of 3‘- and 4‘-substituted flavones in terms of the pharmacophore model has yielded new information for the further development of the pharmacophore model.

The effect of mutating the conserved amino acid residue arginine 120 to lysine in the GABAAreceptor α1subunit was studied. In electrophysiological experiments, the arginine 120 lysine (R120K) mutation in the α1subunit, when co-expressed with β2and γ2subunits in Sf-9 insect cells, induces a 180-fold rightward shift of the GABA dose–response curve compared with wild type α1β2γ2sGABAAreceptors. The diazepam potentiation of GABA-gated chloride ion currents was not affected. The binding of the GABAAligands [3H]muscimol and [3H]SR 95531 to α1(R120K)β2γ2sGABAAreceptors was abolished but the binding affinity of the benzodiazepine receptor ligand [3H]flunitrazepam was unchanged. These results suggest that the arginine residue 120 in the α1subtype of the GABAAreceptor is essential for GABA binding.

Conformationally flexible analogues of the atypical antipsychotic sertindole (1-[2-[4-[5-chloro-1-(4-fluorophenyl)-1H-indol-3-yl]-4-piperidinyl]ethyl]-2-imidazolidinone) were synthesized. Replacement of the 4-piperidinyl ring in sertindole by a 2-(methylamino)ethoxy group or a 2-(methylamino)ethyl group (e.g. 1-[2-[2-[5-chloro-1-(4-fluorophenyl)-1H-indol-3-yloxy]ethylmethylamino]ethyl]-2-imidazolidinone and 1-[3-[[2-[5-chloro-1-(4-fluorophenyl)-1H-indol-3-yl]ethyl]methylamino]propyl]-2-imidazolidinone results in binding affinities for serotonin 5-HT2A and dopamine D2 receptors, as well as α1 adrenoceptors, which are very similar to those of sertindole. (Methylamino)alkyl groups of other chain lengths, 3-(methylamino)propyloxy groups, and 2-(methylamino)ethylsulfanyl groups do not have such properties. The capability of the 2-(methylamino)ethoxy group and the 2-(methylamino)ethyl group to replace the 4-piperidinyl ring in sertindole is reflected in molecular modeling studies using recently published receptor-interaction models for 5-HT2 and D2 receptors. Structure−affinity investigations concerning the substituents in the indole nucleus and the 2-imidazolidinone ring system in the 2-(methylamino)ethoxy and the 2-(methylamino)ethyl analogues of sertindole have led to high affinity serotonin 5-HT2A receptor antagonists with selectivity versus dopamine D2 receptors and α1 adrenoceptors (e.g. 1-[2-[[2-[6-chloro-1-(4-fluorophenyl)-1H-indol-3-yloxy]ethyl]methylamino]ethyl]-2-imidazolidinone and 1-[3-[[2-[6-chloro-1-(4-fluorophenyl)-1H-indol-3-yl]ethyl]methylamino]propyl]-2-imidazolidinone). The latter derivative has also high selectivity for 5-HT2A receptors versus serotonin 5-HT2C receptors. Replacement of the basic amino group by nitrogen-containing six-membered rings has led to 5-chloro-1-(4-fluorophenyl)-3-[(4-methylpiperazinyl)ethoxy]-1H-indole, which has high affinity for dopamine D2, versus low affinity for serotonin 5-HT2A receptors and α1 adrenoceptors.

A large number of substituted chalcones have been synthesized and tested for antileishmanial and lymphocyte-suppressing activities. A subset of the chalcones was designed by using statistical methods. 3D-QSAR analyses using 67 (antileishmanial activity) and 63 (lymphocyte-suppressing activity) of the compounds for the training sets and 9 compounds as an external validation set were performed by using the GRID/GOLPE methodology. The Smart Region Definition procedure with subsequent region selection as implemented in GOLPE reduced the number of variables to approximately 1300 yielding 3D-QSAR models of high quality (lymphocyte-suppressing model, R² = 0.90, Q² = 0.80; antileishmanial model, R² = 0.73, Q² = 0.63). The coefficient plots indicate that steric interactions between the chalcones and the target are of major importance for the potencies of the compounds. A comparison of the coefficient plots for the antileishmanial effect and the lymphocyte-suppressing activity discloses significant differences which should make it possible to design chalcones having a high antileishmanial activity without suppressing the proliferation of lymphocytes.