X-ray crystal structure, partitioning behavior, and molecular modeling study of piracetam-type nootropics: insights into the pharmacophore

The importance of intramolecular hydrogen bonds on the translocation of the small drug piracetam through a lipid bilayer

The number of hydrogen bond donors and acceptors is a fundamental molecular descriptor to predict the oral bioavailability of small drug candidates. In fact, the most widely used oral bioavailability rules (such as the Lipinsky's rule-of-five and the Veber rules) make use of this molecular descriptor. It is generally assumed that hydrogen bond donors and acceptors impact on passive diffusion across cell membranes, a fundamental event during drug absorption and distribution. Although the relationship between the number of these motifs and the probability of having good oral bioavailability has been studied and described for more than 20 years, little attention has been given to their spatial distribution in the molecule. In this paper, we used molecular dynamics to describe the effect of intramolecular hydrogen bonding on the passive diffusion of a small drug (piracetam) through a lipid membrane. The results indicated that the formation of an intramolecular hydrogen bond decreases the barrier for translocation by ca. 4 kcal mol-1 and increases the permeability of the tested molecule, partially compensating the desolvation penalty arising from the penetration of the drug into the biological membrane core. This effect was apparent in simulations where the formation of this interaction was prevented with the help of modified potentials, and in simulations with a similar compound to piracetam that was not able to form this intramolecular hydrogen bond due to a larger distance between the hydrogen bond donor and acceptor groups. These results were also supported by coarse-grained methods, which are becoming an important resource for sampling a larger chemical space of molecules, with reduced computational effort. Furthermore, entropy and enthalpy derived profiles were also obtained as the compounds translocated across the membrane, suggesting that, even though the process of formation of internal hydrogen bonds is entropically unfavorable, the enthalpic gain is such that the formation of these interactions is beneficial for the passive diffusion across cell membranes.

Enantioselective Rh-Catalyzed Carboacylation of C═N Bonds via C-C Activation of Benzocyclobutenones

Herein we describe the first enantioselective Rh-catalyzed carboacylation of oximes (imines) via C-C activation. In this transformation, the benzocyclobutenone C1-C2 bond is selectively activated by a low valent rhodium catalyst and subsequently the resulting two Rh-C bonds add across a C═N bond, which provides a unique approach to access chiral lactams. A range of polycyclic nitrogen-containing scaffolds were obtained in good yields with excellent enantioselectivity. Further derivatization of the lactam products led to a rapid entry to various novel fused heterocycles.

Molecular docking, spectroscopic studies and quantum calculations on nootropic drug

A systematic vibrational spectroscopic assignment and analysis of piracetam [(2-oxo-1-pyrrolidineacetamide)] have been carried out using FT-IR and FT-Raman spectral data. The vibrational analysis was aided by an electronic structure calculation based on the hybrid density functional method B3LYP using a 6-311G++(d,p) basis set. Molecular equilibrium geometries, electronic energies, IR and Raman intensities, and harmonic vibrational frequencies have been computed. The assignments are based on the experimental IR and Raman spectra, and a complete assignment of the observed spectra has been proposed. The UV-visible spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies and the maximum absorption wavelengths λmax were determined by the time-dependent DFT (TD-DFT) method. The geometrical parameters, vibrational frequencies and absorption wavelengths were compared with the experimental data. The complete vibrational assignments are performed on the basis of the potential energy distributions (PED) of the vibrational modes in terms of natural internal coordinates. The simulated FT-IR, FT-Raman, and UV spectra of the title compound have been constructed. Molecular docking studies have been carried out in the active site of piracetam by using Argus Lab. In addition, the potential energy surface, HOMO and LUMO energies, first-order hyperpolarizability and the molecular electrostatic potential have been computed.

(3aS,7aS)-5-[(S)-3,3,3-Trifluoro-2-meth-oxy-2-phenyl-propano-yl]-2,3,4,5,6,7-hexa-hydro-1H-pyrrolo[3,4-c]pyridin-3(2H)-one monohydrate

rac-Benzyl 3-oxohexa­hydro-1H-pyrrolo[3,4-c]pyridine-5(6H)-carboxyl­ate was separated by chiral chromatography, and one of the enanti­omers ([α]²²_D = +10°) was hydrogenated in the presence of Pd/C in methanol, producing octa­hydro-3H-pyrrolo[3,4-c]pyridin-3-one. The latter was reacted with (2R)-3,3,3-trifluoro-2-meth­oxy-2-phenyl­propanoyl chloride [(R)-(−)-Mosher acid chloride], giving rise to the title compound, C₁₇H₁₉F₃N₂O₃·H₂O. The present structure established the absolute configuration of the pyrrolopiperidine fragment based on the known configuration of the (R)-Mosher acid chloride. The piperidine ring has a somewhat distorted chair conformation and is cis-fused with the five-membered envelope-shaped ring; the plane of the exocyclic amide bond is approximately orthogonal to the plane of the phenyl ring, making a dihedral angle of 82.31 (3)°. The water mol­ecule acts as an acceptor to the proton of the amino group in an N—H⋯O inter­action, and as a double proton donor in O—H⋯O hydrogen bonds, generating infinite bands along the a axis.

Solvent Influences on Metastable Polymorph Lifetimes: Real-Time Interconversions Using Energy Dispersive X-Ray Diffractometry**We dedicate this paper to Professor David Grant. Not only a talented scientist, he was a man who gave freely of his time and ideas to support and encourage others, including ourselves

Solvent influences on the crystallization of polymorph and hydrate forms of the nootropic drug piracetam (2-oxo-pyrrolidineacetamide) were investigated from water, methanol, 2-propanol, isobutanol, and nitromethane. Crystal growth profiles of piracetam polymorphs were constructed using time-resolved diffraction snapshots collected for each solvent system. Measurements were performed by in situ energy dispersive X-ray diffraction recorded in Station 16.4 at the synchrotron radiation source (SRS) at Daresbury Laboratory, CCLRC UK. Crystallizations from methanol, 2-propanol, isobutanol, and nitromethane progressed in a similar fashion with the initial formation of form I which then converted relatively quickly to form II with form III being generated upon further cooling. However, considerable differences were observed for the polymorphs lifetime and both the rate and temperature of conversion using the different solvents. The thermodynamically unstable form I was kinetically favored in isobutanol and nitromethane where traces of this polymorph were observed below 10 degrees C. In contrast, the transformation of form II and subsequent growth of form III were inhibited in 2-propanol and nitromethane solutions. Aqueous solutions produced hydrate forms of piracetam which are different from the reported monohydrate; this crystallization evolved through successive generation of transient structures which transformed upon exchange of intramolecular water between the liquid and crystalline phases.

Imidazole H3-antagonists: relationship between structure and ex vivo binding to rat brain H3-receptors

H3-antagonists possess promising pharmacological effects on awakening, learning and memory, but few data on their access to the central nervous system (CNS) have been reported so far. The purpose of this work was to investigate the relationships between structure and brain penetration of a series of H3-antagonists, using ex vivo binding experiments in rats. H3-antagonists belonging to different chemical classes but all having an imidazole ring, an alkyl spacer, a polar fragment and a lipophilic ending group, were selected among the numerous H3-antagonists recently described by us. Ex vivo binding studies were performed by inhibiting specific [3H]-(R)-alpha-methylhistamine ([3H]-RAMHA) binding to rat cerebral cortical membranes following H3-antagonist peripheral administration. Ionization constants and partition coefficients in n-octanol/water and 1,2-dichloroethane/water were determined by the potentiometric pH-metric method and were compared to the ex vivo binding potencies to analyse structure-property relationships (SPR). In the ex vivo assay, the H3-antagonists showed different potencies (pED50) not correlated to their in vitro H3-receptor binding affinities (pKi). Compound 4a, having a benzothiazol-2-yl-thioethyl chain, showed high ex vivo potency (ED50=1.35 mg kg(-1) i.p.) and a fast brain penetration, eliciting maximal displacement of [3H]-RAMHA already 5 min after i.v. or i.p. administration. Ex vivo binding assays of three compounds, following i.v. and i.p. administration, showed that the observed i.p. ex vivo potencies were not significantly affected by biotransformation. Within the set of compounds, those having a better ability to reach the CNS had a logDoct(7.4) in the range 2-3.5, and a DeltalogPoct-dce < 2. The combined use of two easily measurable physicochemical descriptors, namely logDoct(7.4) (apparent lipophilicity at pH 7.4) and DeltalogPoct-dce (a descriptor of H-bond donor capacity) allowed to model brain permeation of the majority of the compounds examined.

A Quenched Molecular Dynamics−Rotating Frame Overhauser Spectroscopy Study of a Series of Semibiosynthetically Monoacylated Anthocyanins

Quenched molecular dynamics (QMD), in conjunction with NMR (ROESY) studies, was used to investigate the conformational behavior of some semibiosynthetic anthocyanins of the type 6-O-acyl-beta-D-Glcp-(166)-beta-D-Galp-(1-->O(3))-cyanidin, with and without a beta-D-Xylp branch at the 2-O-Gal position. These compounds, which are produced by the addition of selected carboxylic acids to growing tissue cultures of Daucus carota (wild carrot), are of interest as color-stabilized anthocyanins, some of which have potential as useful colorants in the nutraceutical and pharmaceutical industries. The QMD-ROESY studies, performed for the first time on anthocyanins, have led to the identification of families of conformers of these flexible molecules that are of interest in work toward determining the mechanism for stabilization of color among these compounds in solution.

2-pyrrolidinone moiety is not critical for the cognition-enhancing activity of piracetam-like drugs

Following the indications of previous work, 2-pyrrolidinone moiety of piracetam and piracetam-like compounds has been opened to the corresponding amide derivatives. As found previously in the case of 1,4-diazabicyclo[4.3.0]nonan-9-one compounds, the cognition-enhancing activity of 2-pyrrolidinone compounds is maintained in most cases, suggesting that this moiety is not crucial for activity.

Development of molecular hydrogen-bonding potentials (MHBPs) and their application to structure-permeation relations

Hydrogen bonds are major forces of recognition in biochemistry and molecular pharmacology; they are an essential component of intermolecular interactions and determine to a significant extent the 3D-structure of bio-macromolecules. To explore three-dimensional H-bonding properties, a new tool called Molecular Hydrogen-Bonding Potentials (MHBPs) was created. The development of this tool is based on a stepwise procedure similar to the one used successfully to generate the Molecular Lipophilicity Potential (MLP). First, a H-bonding fragmental system was developed starting from published solvatochromic parameters. An atomic H-bonding donor fragmental value (alpha) is associated to each hydrogen atom in a polar moiety. Similarly, an atomic H-bonding acceptor fragmental value (beta) is associated to each polar atom. A distance function and an angle function were defined to take into account variations of the MHBPs in space. The fragmental system and the geometric functions were then combined to generate the MHBPs. These are calculated at each point of an adequate molecular surface or on a three-dimensional grid. The MHBPs were compared with GRID interactions energies and correlated with success to oral drug absorption data. Available examples demonstrate that the MHBPs are a promising computational tool in drug design. Their combination with CoMFA and VolSurf is being studied.

Design, synthesis, and preliminary pharmacological evaluation of 1, 4-diazabicyclo[4.3.0]nonan-9-ones as a new class of highly potent nootropic agents

Several 4-substituted 1,4-diazabicyclo[4.3.0]nonan-9-ones have been synthesized and tested in vivo on mouse passive avoidance test, to evaluate their nootropic activity. The results show that they represent a new class of nootropic drugs with a pharmacological profile very similar to that of piracetam, showing much higher potency with respect to the reference. Among the compounds studied, 7 (DM 232) shows outstanding potency, being active at the dose of 0. 001 mg kg(-1) sc.

QSAR analysis of Delta(8)-THC analogues: relationship of side-chain conformation to cannabinoid receptor affinity and pharmacological potency

A novel quantitative structure-activity relationship (QSAR) for the side-chain region of Delta(8)-tetrahydrocannabinol (Delta(8)-THC) analogues is reported. A series of 36 side-chain-substituted Delta(8)-THCs with a wide range of pharmacological potency and CB1 receptor affinity was investigated using computational molecular modeling and QSAR analyses. The conformational mobility of each compound's side chain was characterized using a quenched molecular dynamics approach. The QSAR techniques included a modified active analogue approach (MAA), multiple linear regression analyses (MLR), and comparative molecular field analysis (CoMFA) studies. All three approaches yielded consistent results. The MAA approach applied to a set of alkene/alkyne pairs identified the most active conformers as those with conformational mobility constrained within an approximately 8 A radius. MLR analyses (restricted to 15 hydrocarbon side-chain analogues) identified two variables describing side-chain length and terminus position that were able to fit the pharmacological data for receptor affinity with a correlation coefficient for pK(D) of 0.82. While chain length was found to be directly related to receptor affinity, the angle made by the side chain from its attachment point to its terminus (angle defined by C3-C1'-side-chain terminus carbon, see Figure 1) was found to be inversely related to affinity. These results suggest that increased side-chain length and increased side-chain ability to wrap around the ring system are predicted to increase affinity. Therefore, the side chain's conformational mobility must not restrict the chain straight away from the ring system but must allow the chain to wrap back around toward the ring system. Finally, the CoMFA analyses involved all 36 analogues; they also provided data to support the hypothesis that for optimum affinity and potency the side chain must have conformational freedom that allows its terminus to fold back and come into proximity with the phenolic ring.

Determination of possible impurities in piracetam using FTIR spectroscopy

Piracetam (2-oxo-1-pyrrolidine acetamide (PAm)) may contain some structurally related impurities deriving from synthesis or degradation, mainly 2-oxo-1-pyrrolidine acetic acid (PAc). A rapid and sensitive Fourier transform infrared (FTIR) spectrophotometric method was developed for determination of possible impurities in piracetam. The results showed that the method was effective for the simultaneous determination of PAc in piracetam by FTIR spectrophotometry and may be a real alternative to HPLC. The apparent spectral resolution was first enhanced by using the Fourier self-deconvolution (FSD) method and the profiles were then fully deconvoluted by using a curve fitting procedure. FSD method followed by curve fitting allowed to evaluate quantitatively the areas under the pyrrolidine acetic acid peaks. Mixtures of known composition were used as standards to minimise errors due to the presence of both compounds in the same mixture. The detection limit of pyrrolidine acetic acid was estimated to be 0.1% with respect to piracetam.

Application of neural networks in structure-activity relationships

Methodology and application of artificial neural networks in structure-activity relationships are reviewed focusing on the most frequently used three-layer feedforward back-propagation procedure. Two applications of neural networks are presented and a comparison of the performance with those of CoMFA and a classical QSAR analysis is also discussed.

Production and characterization of 22 monoclonal antibodies directed against S 20499, a new potent 5-HT1A chiral agonist: influence of the hapten structure on specificity and stereorecognition

PURPOSE

An immunoconjugate model was proposed to produce stereoselective monoclonal antibodies (MAbs) for the quantitation of a 5-HT1A agonist, S 20499. MAbs produced were characterized in terms of stereoselectivity and specificity towards the opposite enantiomer and structural analogs.

METHODS

The immunogen was formed following the effective addition of a butanoic acid spacer arm between the parent S 20499 structure and bovine serum albumin (BSA). After fusion (modified Köhler and Milstein's procedure), specificity of MAbs was obtained using the Abraham's criteria. Experimental and calculated partition coefficients were determined.

RESULTS

Twenty-two hybridoma cell lines were established secreting MAbs (apparent association constants ranging from 1.1 x 10(8) to 2.8 X 10(9) M(-1)). Several MAbs showed cross-reactivity levels of less than 5% with S 20500 (optical antipode), which could allow a stereospecific assay to be set up. Both chroman and azaspiro moieties were part of the epitopic site. Dealkylation and hydroxylation(s) led to various crossreactivity levels. Four antibody families were described in terms of specificity.

CONCLUSIONS

This study highlighted the influence of the immunoconjugate construction (coupling site and type of spacer arm) in the immuno-stereospecificity of Abs. The results obtained for two monohydroxylated metabolites suggest that the lipophilicity behavior could be a valuable tool for predicting Ab-crossreactivity.

Mechanisms of liposomes/water partitioning of (p-methylbenzyl)alkylamines

PURPOSE

The objective of this study was to compare and interpret the variations in lipophilicity of homologous (p-methylbenzyl)alkylamines (MBAAs) in isotropic (octanol/water) and anisotropic (zwitterionic liposomes/water) system.

METHODS

Two experimental approaches were used, namely the pH-metric method to measure lipophilicity parameters in octanol/water and liposomes/water systems, and changes in NMR relaxation rates to validate the former method and to gain additional insights into the mechanisms of liposomes/water partitioning.

RESULTS

For long-chain homologues (N-butyl to N-heptyl), the octanol/water and liposomes/water systems mostly expressed hydrophobicity. In contrast, the lipophilicity of the shorter homologues (N-methyl to N-propyl) in the two systems expressed various electrostatic and polar interactions.

CONCLUSIONS

The study sheds light on the molecular interactions between zwitterionic liposomes and amphiphilic solutes in neutral and cationic form.

Molecular properties and pharmacokinetic behavior of cetirizine, a zwitterionic H1-receptor antagonist

The ionization and lipophilicity behavior of the antihistamine (H1-receptor antagonist) cetirizine was investigated, showing the drug to exist almost exclusively as a zwitterion in the pH region 3.5-7.5. In this pH range, its octanol/water lipophilicity is constant and low compared to cationic antihistamines (log D = log PZ = 1.5), whereas its H-bonding capacity is relatively large (delta log PZ > or = 3.1). Conformational, electronic, and lipophilicity potential calculations revealed that zwitterionic cetirizine experiences partial intramolecular charge neutralization in folded conformers of lower polarity. Pharmacokinetic investigations have shown the drug to be highly bound to blood proteins, mainly serum albumin, and to have a low brain uptake, explaining its lack of sedative effects. As such, cetirizine does not differ from "second-generation" antihistamines. In contrast, its very low apparent volume of distribution in humans (0.4 L kg-1, smaller than that of exchangeable water) implies a low affinity for lean tissues such as the myocardium and is compatible with the absence of cardiotoxicity of the drug. The zwitterionic nature and modest lipophilicity of cetirizine may account for this pharmacokinetic behavior. The suggestion is offered that cetirizine and analogous zwitterions, whose physicochemical, pharmacokinetic, and pharmacodynamic properties differ from those of "first-" and "second-generation" drugs in this class, could be considered as "third-generation" antihistamines.

Nonionic compact dimers: a new generation of isosmolar iodinated contrast media with low viscosity

RATIONALE AND OBJECTIVES

The authors evaluated compact dimers, a new class of molecule designed to reduce the osmolality of concentrated solutions of x-ray contrast media without increasing their viscosity.

MATERIALS AND METHODS

Molecular modeling was used to design a new hexaiodo dimeric structure with low viscosity and good shielding of hydrophobic areas. This design ends in the synthesis of different prototypes, the structure of which was characterized by a single bond between two perpendicular rings and the presence of tertiary amides. The validity of this approach was investigated with measurements of physicochemical properties (viscosity, osmolality, logP) and pharmacologic studies (urinary and biliary excretion, intravenous and intracerebral medial lethal dose).

RESULTS

Solutions of the compact dimers at a concentration of 350 mg of iodine per milliliter combine osmolalities that are close to that of blood with viscosities at ambient temperature nearly half those of commercially available dimers. Furthermore, these new compounds have a tolerance level comparable with that of currently used nonionic media (intravenous median lethal dose, > 17.5 g of iodine per kilogram).

CONCLUSION

The three-dimensional structure of the compact dimers has made it possible to control both physicotoxicity and chemotoxicity by combining isotonicity and low viscosity with good tolerance.

Estimation of partitioning parameters of nonionic surfactants using calculated descriptors of molecular size, polarity, and hydrogen bonding

A study was carried out to verify the capacity of the Abraham's solute descriptors (R2, an excess molar refraction; pi 2H, the dipolarity/polarizability; sigma alpha 2H and sigma beta 2H, the summation hydrogen-bond acidity and basicity; and Vx, the characteristic volume of McGowan) to predict the alkane-water partition coefficient (log Palk) of nonionic surfactants. Log P values were taken from the literature and examined for linear solvation energy-related (LSER) equations with calculated physicochemical descriptors. A stepwise multiple linear regression (MLR) analysis allowed us to derive LSER models which, unlike those previously published for a standard set of solutes, revealed that R2 and sigma beta 2H are the major contributors to log Palk. A minor contribution of Vx was also detected, whereas surprisingly sigma alpha 2H required a positive coefficient. The less relevant size effect seems to indicate that for nonionic surfactants the energy needed for creating a water cavity is largely compensated for by the favorable interactions of ethoxy groups in the polar chain with water, whereas the log P-increasing effect of hydrogen-bond donor groups could be explained by considering the occurrence of folded, more lipophilic conformers, favored by the formation of intramolecular hydrogen bonds in the apolar phase. This hypothesis was substantiated by the calculation of the molecular lipophilicity potential on the water-accessible surface of extended and folded conformers of two representative surfactants, selected by high-temperature molecular dynamics. Besides MLR, a principal component analysis on a larger set of descriptors, comprising three solubility parameters (delta D, based on dispersion forces; delta H, including the contribution of hydrogen bonding; delta O, overall solubility parameter) afforded the so-called principal properties, which were able to characterize nonionic surfactants and to satisfactorily assess their lipophilicity-related properties.

TRH mimetics: differentiation of antiamnesic potency from antidepressant effect

For the purpose of rational modification of the TRH molecule, we were pursuing an approach that consists of two steps: (1) 'obligatory' replacement of histidine with glutamine in TRH and (2) the application of conformational constraints for putative bioactive conformation I stabilized by an intramolecular hydrogen bond between C-terminal carboxamide proton and alpha-carbonyl of histidyl (glutaminyl), and conformation II formed by an intramolecular hydrogen bond between alpha-carbonyl of pyroglutamyl and prolinamide proton. Significant antiamnesic potency was discovered in the passive avoidance test (ECS and Scopolamine induced amnesia) for conformation II mimic (8S,10aS)-8-carbamoyl-1,2,3,6,7,8,9,10a- octahydro-5H,10H-pyrrolo[1,2-a][1,4]diazocin-5,10-dione (2) at doses of 0.1 and 1.0 mg/kg. EEG analysis indicates a mild activating effect of compound 2 on EEG, which is similar to that of piracetam and differs from hard amphetamine activation. Conformation I mimic 3-(2-carbamoylethyl)-2,3,6,7,8,8a-hexahydro-1H,4H-pyrrolo[1,2-a] pyrazin-1,4-dione (1) exhibited an antidepressant effect at a dose of 1 mg/kg. The transition from two putative quasi-cyclic bioactive conformations of TRH and its obligatory similar analogue [Gln2]-TRH to their cyclic mimics led to differentiation of antiamnesic and antidepressant activity of TRH.