Chemoinformatics - predicting the physicochemical properties of 'drug-like' molecules.

A few major advances have occurred in the area of physicochemical modeling of organic compounds during the past several years, spurred on by changes in the pharmaceutical industry. Recent advances include the ability to categorize and screen the overall physicochemical properties of potential drug candidates based entirely on their molecular structures and the ability to model the components that contribute to the oral absorption characteristics of potential drug candidates.

Antagonism of baclofen-induced depression of whole-cell synaptic currents in spinal dorsal horn neurones by the potent GABAB antagonist CGP55845.

The potencies of two GABAB receptor antagonists P-[3-aminopropyl]- P-diethoxymethyl-phosphinic acid (CGP35348) and the novel compound 3-N[1-(S)-(3,4-dichlorophenyl)ethyl]amino-2-(S)-hydroxypropyl-P- benzyl-phosphinic acid (CGP55845) have been compared in an in vitro spinal cord preparation. They have been tested as antagonists of baclofen-induced depression of EPSCs of patch-clamped dorsal horn neurons following electrical stimulation of dorsal roots. Mean EC50 values for the depressant action of baclofen were increased by 50- and 140-fold respectively in the presence of CGP35348 (200 microM) (n = 5) and CGP55845 (100 nM) (n = 4). This potency of CGP55845 is > 1000-fold higher than that reported previously for other GABAB receptor antagonists.

Computation of brain-blood partitioning of organic solutes via free energy calculations.

The ratio of brain-blood partitioning, log(Cbrain/Cblood) (log BB), of a series of compounds that range from simple solutes to histamine H2 antagonists was correlated with computed solvation free energy in water (delta G degree W). The free energies were computed with the AMSOL 5.0 program using the AM1-SM2.1 solvation model. From a set of 55 compounds, a function was developed in which log BB was related to the free energy of solvation as follows: log BB = 0.054 delta G degree W + 0.43 (r = 0.82 and standard error = 0.41). This correlation provided successful prediction of brain-blood partitioning for compounds outside the training dataset. Furthermore, for a set of 10 drugs, delta G degree W correlated well with literature data for the permeability of endothelial cell monolayers from bovine brain microvessels. In neuroscience drug discovery, the use of computed solvation free energies to predict brain penetration provides a facile method for prioritizing synthetic targets.

Glucose transport-enhancing and hypoglycemic activity of 2-methyl-2-phenoxy-3-phenylpropanoic acids.

A series of 2-phenoxy-3-phenylpropanoic acids has been prepared which contains many potent hypoglycemic agents as demonstrated by assessing glucose lowering in ob/ob mice. Some compounds (32, 33, 59) normalize plasma glucose in this diabetic model at doses of approximately 1 mg/kg. The mechanism of action of these drugs may involve enhanced glucose transport, especially in fat cells, but the compounds do not stimulate GLUT4 translocation and do not increase the levels of GLUT1 or GLUT4 in vivo. Thus, these compounds may enhance the intrinsic activity of the glucose transporter GLUT1 or GLUT4. Some compounds also modestly decrease hepatocyte gluconeogenesis in vitro, but this is not likely to be a major contributor to the hypoglycemic effect observed in vivo. Likewise, a modest decrease in food consumption observed with some of these compounds was shown by a pair-feeding experiment not to be the primary cause of the hypoglycemia observed.

Quinazolin-4-one alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor antagonists: structure-activity relationship of the C-2 side chain tether.

A series of 6-fluoro-3-(2-chlorophenyl)quinazolin-4-ones has been prepared, which contains a 2-fluorophenyl ring attached to C-2 by a variety of two-atom tethers. These compounds were used to probe the structure-activity relationship (SAR) for AMPA receptor inhibition. The relative potencies of the new compounds ranged from 11 nM to greater than 10 microM. The differential activity of the compounds was rationalized on the basis of alterations of the 2-fluorophenyl positioning (planar and radial) relative to the quinazolin-4-one ring based on computational methods. From this effort, new AMPA receptor antagonists, containing the methylamino tether group, have been identified.

Novel benzisoxazole derivatives as potent and selective inhibitors of acetylcholinesterase.

A series of N-benzylpiperidine benzisoxazoles has been developed as potent and selective inhibitors of the enzyme acetylcholinesterase (AChE). The benzisoxazole heterocycle was found to be an appropriate bioisosteric replacement for the benzoyl functionality present in the N-benzylpiperidine class of inhibitors. The title compounds were synthesized by alkylating 3-methyl-1,2-benzisoxazoles with an iodo piperidine derivatives as the key step. Benzisoxazoles 1b-j,o displayed potent inhibition of AChE in vitro with IC50's = 0.8-14 nM. Particularly interesting were N-acetyl and morpholino derivatives 1g (IC50 = 3 nM) and 1j (IC50 = 0.8 nM), respectively, which displayed outstanding selectivity for acetyl-over butyrylcholinesterase, in excess of 3 orders of magnitude. N-Acetyl 1g also displayed a favorable profile in vivo. This analog showed a dose-dependent elevation of total acetylcholine in mouse forebrain after oral administration with an ED50 = 2.4 mg/kg. In addition, 1g was able to reverse amnesia in a mouse passive avoidance model at doses of 3.2 and 5.6 mg/kg with an average reversal of 89.7%. Molecular dynamics simulations were used to study the possible binding modes of N-benzylpiperidine benzisoxazoles to AChE from Torpedo californica. Key structural insights were obtained regarding the potency of this class of inhibitors. Specifically, Asp-72, Trp-84, Trp-279, Phe-288, and Phe-330 are implicated in the binding of these inhibitors. The N-benzylpiperidine benzisoxazoles may be suitable compounds for the palliative treatment of Alzheimer's Disease.

(3R,4S)-3-[4-(4-fluorophenyl)-4-hydroxypiperidin-1-yl]chroman-4,7-diol: a conformationally restricted analogue of the NR2B subtype-selective NMDA antagonist (1S,2S)-1-(4-hydroxyphenyl)-2-(4-hydroxy-4-phenylpiperidino)- 1-propanol.

(1S,2S)-1-(4-Hydroxyphenyl)-2-(4-hydroxy-4-phenylpiperidino)-1-propanol (CP-101,606, 1) is a recently described antagonist of N-methyl-D-aspartate (NMDA) receptors containing the NR2B subunit. In the present study, the optimal orientation of compounds of this structural type for their receptor was explored. Tethering of the pendent methyl group of 1 to the phenolic aromatic ring via an oxygen atom prevents rotation about the central portion of the molecule. Several of the new chromanol compounds have high affinity for the racemic [3H]CP-101,606 binding site on the NMDA receptor and protect against glutamate toxicity in cultured hippocampal neurons. The new ring caused a change in the stereochemical preference of the receptor-cis (erythro) compounds had better affinity for the receptor than the trans isomers. Computational studies suggest that steric interactions between the pendent methyl group and the phenol ring in the acyclic series determine which structures can best fit the receptor. The chromanol analogue, (3R,4S)-3-[4-(4-fluorophenyl)-4-hydroxypiperidin-1- yl]chroman-4,7-diol (12a, CP-283,097), was found to possess potency and selectivity comparable to CP-101,606. Thus 12a is a new tool to explore the function of the NR2B-containing NMDA receptors.

A quantitative study of the actions of excitatory amino acids and antagonists in rat hippocampal slices.

1. A quantitative pharmacological investigation of the actions of excitatory amino acids on hippocampal CA1 neurones has been made using a new slice preparation developed for grease gap recording; d.c. potential was measured across a grease barrier placed between alvear fibres and the bathing medium. 2. In Mg2+-free perfusate, N-methyl-D-aspartate (NMDA, 1-100 microM), quisqualate (1-500 microM), kainate (1-200 microM) and alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA, 1-100 microM) caused dose-dependent depolarizations. 3. The dose-response relationships were fitted to logistic expressions. The maximum responses to AMPA, NMDA and kainate were similar; their respective EC50 values were 5, 13 and 23 microM. Quisqualate had a smaller maximum; its EC50 value was 10 microM. The slopes of the dose-response relationships were different for the 4 agonists; the order of steepness of the slopes was NMDA greater than AMPA greater than kainate greater than quisqualate. 4. Similar amino acid-induced depolarizations were observed in slices of just the CA1 region or in whole slices bathed in tetrodotoxin. Isolated alvear fibres, however, were insensitive to the excitatory amino acids. 5. D-2-Amino-5-phosphonovalerate (APV, 50 microM) selectively and reversibly antagonized responses induced by NMDA (apparent pA2 = 5.21). 6. Kynurenic acid (1 mM) reversibly depressed responses to the three agonists tested. The dose-ratios for antagonism of AMPA, kainate and quisqualate were 6.9, 5.6 and 4.6 respectively. 7. This preparation has a different sensitivity profile to agonists from those of previously reported preparations of spinal cord, neocortex and cerebellum. The greater sensitivity to NMDA may be due to the higher density of NMDA receptors in the hippocampus. The effects of the antagonists, APV and kynurenate, are similar to those found in other brain areas.

The effect of nicotine on motoneurones of the immature rat spinal cord in vitro.

Nicotine [(-)-nicotine di(+)-tartrate 1-50 microM] produced depolarization of motoneurones as recorded from ventral roots of immature (1-5 day old) rat hemisected spinal cord preparations. This action of nicotine was accompanied by marked desensitization which persisted for at least 2 h following a 2 min application. Ventral roots sectioned from the spinal cord, which were sensitive to glycine, failed to respond to nicotine. Blockade of regenerative electrical activity with tetrodotoxin produced a mean reduction of 39% in the response to 10 microM nicotine. In order to avoid desensitization, blocking agents were tested for their ability to suppress the initial response to a 2 min application of 10 microM nicotine (0.58 mV +/- 0.07 s.e. mean, 21 preparations) in 4 or more naïve preparations. Responses to nicotine (10 microM) were significantly reduced by 10 microM hexamethonium and were abolished by 250 microM hexamethonium but were resistant to the following antagonists:- atropine (1 microM), phentolamine (2 microM), strychnine (10 microM), kynurenic acid (2 mM) and a mixture of bicuculline (50 microM) and picrotoxin (50 microM). It is concluded that the depolarizing responses to nicotine may be due to the presence of nicotinic receptors either on the motoneurone membrane or on nerve terminals adjacent to motoneurones which release an unidentified neurotransmitter.

6-Cyano-7-nitroquinoxaline-2,3-dione as an excitatory amino acid antagonist in area CA1 of rat hippocampus.

1. A quantitative pharmacological investigation of the excitatory amino acid antagonist 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX) has been made in area CA1 of rat hippocampal slices bathed in 1 mM Mg2+ containing medium. 2. At a concentration of 10 microM, CNQX reversibly antagonized responses to alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA), quisqualate and kainate; it produced a parallel shift in their log dose-response curves. Responses to N-methyl-D-aspartate (NMDA) were not antagonized by 10 microM CNQX (dose-ratio: 1.04 +/- 0.06, n = 3). 3. Schild plots (constructed over the range 1-100 microM) yielded the following estimated pA2 values, AMPA 5.8, quisqualate 5.9, and kainate 5.9. NMDA was antagonized by 100 microM CNQX, giving an apparent log K of 4.44 +/- 0.06. 4. The slopes (+/- s.e. mean) of the Schild plots were for AMPA 0.84 +/- 0.06, quisqualate 0.79 +/- 0.04 and kainate 0.68 +/- 0.07. These were all significantly less than unity. 5. Synaptic responses elicited by low frequency activation of the Schaffer collateral-commissural pathway were blocked completely by CNQX (10 microM) providing that a low stimulus intensity was used. With high intensity stimulation a small component remained that was blocked by the selective NMDA antagonist D-2-amino-5-phosphonovalerate (APV). 6. These results suggest that CNQX does not differentially affect the responses of CA1 neurones to AMPA, quisqualate and kainate. It does, however, depress responses to these agonists to a greater degree than it does responses to NMDA and it is a highly effective synaptic antagonist.

Electrogenic uptake contributes a major component of the depolarizing action of L-glutamate in rat hippocampal slices.

1. A grease-gap technique has been used to measure d.c. potentials, in response to the application of excitatory amino acids and electrical stimulation of the Schaffer collateral-commissural pathway, in the CA1 region of rat hippocampal slices. The actions of L-glutamate (L-Glu) have been quantified and compared to those of structurally related compounds. 2. Perfusion of L-Glu (90s applications) depolarized the tissue with a threshold of approximately 50 microM and a maximum response in excess of 10 mM. L-Aspartate (L-Asp) produced a similar dose-response relationship. By comparison N-methyl-D-aspartate (NMDA) and alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) were more potent excitants, producing dose-dependent depolarizations over the range 2-50 microM. 3. Application of the agonists depressed the amplitude of electrically-evoked synaptic responses; an effect that presumably reflects depolarization of neuronal tissue. However, for a given agonist-induced d.c. potential. L-Glu or L-Asp caused smaller depressions of synaptic responses than did either NMDA or AMPA. 4. The combined application of 50 microM D-2-amino-5-phosphonopentanoate (AP5) and 10 microM 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX) substantially depressed synaptic responses and antagonized responses to NMDA and AMPA producing mean (+/- s.e.) dose-ratios of 12.2 +/- 1.2 and 7.0 +/- 0.8, respectively. However, these compounds produced minimal antagonism of responses to L-Glu and L-Asp (dose-ratios of 1.5 +/- 0.1 and 1.5 +/- 0.2, respectively). 5. Responses to the stereoisomers of homocysteate (HCA) were compared over the range 50 microM to 10 mM. D-HCA was approximately 3.6 times more potent than L-HCA and was antagonized to a greater extent by the combined application of 50 microM AP5 and 10 microM CNQX; the dose ratios were 8.7 + 0.8 and 5.1 + 0.9 for the D- and L- isomers, respectively. 6. The application of high doses of an excitant (e.g., 50mM L-Glu or 5mM D-HCA) caused an irreversible loss of sensitivity to NMDA and AMPA and abolished synaptic transmission. Responses to the other excitants were depressed by this excitotoxic lesion in the following order: D-HCA > L-HCA > L-Glu = LAsp. In slices treated in this manner, L-Glu, L-Asp and L-HCA produced very similar dose-response curves. 7. Some slices were unresponsive to NMDA, AMPA and electrical stimulation from the onset of the experiment but had sensitivity to L-Glu, L-Asp and L-HCA similar to that of slices that had received an excitotoxic lesion. 8. Slices that were experimentally lesioned, such that they became unresponsive to synaptic stimulation, AMPA and NMDA, were depolarized by a variety of compounds when tested at 5 mm. The D- and L- enantiomers of Asp and Glu produced similar responses and were slightly more active than quisqualate and threo-hydroxy-L-aspartate (THLA). Glycine, L-serine, D-serine, L-alanine and 4-aminobutanoate (GABA) elicited responses 15-30% of the size, while L-lysine, alpha-amino-isobutanoate and L-proline produced depolarizations of less than 10% of the size of those induced by 5mM L-Glu. NMDA and dihydrokainate were either inactive or induced small negative shifts in the d.c. potential. 9. We conclude that when hippocampal slices are perfused with L-Glu (or L-Asp) the main source of the depolarization is due to an interaction with an electrogenic carrier system.

Ring closing metathesis mediated synthesis of 4a-aryloxodecahydroisoquinolines, intermediates in the preparation of novel opiates.

[reaction: see text]. The concise syntheses of the 4a-aryldecahydroisoquinolines 1 and 2 through a uniform strategy starting from N-methyl-3-allyl-4-piperidinone are reported in this Letter. Key transformations include a ring closing metathesis reaction to prepare a trans-octahydroisoquinoline common intermediate and a regiocontrolled hydroboration-oxidation sequence.

CNQX blocks acidic amino acid induced depolarizations and synaptic components mediated by non-NMDA receptors in rat hippocampal slices.

6-Cyano-2,3-dihydroxy-7-nitro-quinoxaline (CNQX; FG 9065) is a new excitatory amino acid antagonist. In the spinal cord it has been reported to selectively block responses to acidic amino acids acting at receptors of the non-N-methyl-D-aspartate (non-NMDA) type. Here we report that in rat hippocampal slices bathed in Mg2+-free medium 10 microM CNQX reversibly blocks responses to alpha-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA), quisqualate and kainate but not NMDA. The synaptic response evoked by low frequency stimulation of Schaffer collateral-commissural fibres in 1 mM Mg2+-containing medium is completely blocked by this concentration of CNQX. In contrast the synaptic response evoked in Mg2+-free medium is not fully blocked by CNQX. The CNQX-insensitive component is, however, abolished by addition of a selective NMDA antagonist. The use of CNQX has allowed for the first time selective synaptic activation of NMDA receptors in the hippocampus.

Visualizing substructural fingerprints.

Substructural fingerprints have proven very useful for chemical library and diversity analysis, but their high dimensionality makes them poorly suited to principal components analysis and to standard nonlinear mapping methods. By using a combination of optimizable K-dissimilarity selection (OptiSim) and a modified stress function that suppresses effects of distances that fall beyond a characteristic horizon, it is possible to relax principal components analysis coordinates into more consistently meaningful projections from fingerprint space into two dimensions. The nonlinear maps so obtained are useful for characterizing combinatorial libraries, for comparing sublibraries, and for exploring the distribution of biological properties across structural space.

Inclusion complexation of ziprasidone mesylate with beta-cyclodextrin sulfobutyl ether.

Ziprasidone is an antipsychotic agent indicated primarily for the treatment of schizophrenia. An intramuscular dosage form of ziprasidone was developed using beta-cyclodextrin sulfobutyl ether (SBECD) to solubilize the drug by complexation. Inclusion complexation of ziprasidone mesylate (ZM) with SBECD was studied by circular dichroism (CD) spectroscopy, proton nuclear magnetic resonance (1H NMR) spectroscopy, Monte Carlo simulations, phase-solubility studies, and counterion titration. The results of the studies indicate that ZM, of which the counterion is not fully dissociated from the drug, forms a 1:1 inclusion complex with SBECD with the benzisothiazole group positioned in the cavity. A mathematical model was developed to calculate stability constants of inclusion complexes for the ion pair (Z+M-:SBECD) and the dissociated ionic form (Z+:SBECD) of ZM; the values were 7892 and 957 M(-1), respectively. The model also allowed the dissociation constants of noncomplexed and complexed ZM to be calculated; the value of the former is 8-fold greater than the value of the latter. These results indicate that the inclusion complex formation of the ion pair is favored over that of the dissociated ionic form of ZM, and that the dissociation of ZM is suppressed by inclusion complexation with SBECD.

Involvement of excitatory amino acid receptors in long-term potentiation in the Schaffer collateral-commissural pathway of rat hippocampal slices.

The present article reviews studies from our laboratory, which have shown that excitatory amino acids receptors of the N-methyl-D-aspartate type are involved in the induction of long-term potentiation in the Schaffer collateral-commissural pathway of rat hippocampal slices. The nature of the excitatory amino acid receptors that mediate the response that is modified by the induction of long-term potentiation is also considered. The mechanism of induction of long-term potentiation is discussed, as are some possible stages that are required for the maintenance of this process. Some new data are presented concerning the ability of N-methyl-D-aspartate to potentiate synaptic transmission and to depress the amplitude of the presynaptic fibre volley. Concerning the potentiation, it is shown that brief (1-2 min) perfusion of slices with N-methyl-D-aspartate is sufficient to potentiate synaptic transmission for at least 3 h. The N-methyl-D-aspartate induced depression of the presynaptic fibre volley is shown to be transient and independent of synaptic transmission.

Design, synthesis and biological evaluation of 3-amino-3-phenylpropionamide derivatives as novel mu opioid receptor ligands.

3-Amino-3-phenylpropionamide derivatives were produced as small molecule mimics of the cyclic octapeptide octreotide from readily available imine 1. The compounds exhibit high affinity for the mu opioid receptor.

Inhibition of MMP-1 and MMP-13 with phosphinic acids that exploit binding in the S2 pocket.

Through the use of empirical and computational methods, phosphinate-based inhibitors of MMP-1 and MMP-13 that bind into the S2 pocket of these enzymes were designed. The synthesis and testing of 2 suggested that binding was occurring as hypothesized. Structure determination of a co-crystal of 2 bound to the catalytic domain of MMP-1 confirmed the binding mode. Substituents binding into S2, S1', S2' and S3', were optimized yielding compounds with low double-digit nM IC50's against these enzymes.