Molecular level model for the agonist/antagonist selectivity of the 1,4-dihydropyridine calcium channel receptor

Summary Crystal structures of the 1,4-dihydropyridine (1,4-DHP) calcium channel activators Bay K 8643 [methyl 1,4-dihydro-2,6-dimethyl-3-nitro-4-(3-nitrophenyl)-pyridine-5-carboxylate], Bay O 8495 [methyl 1,4-dihydro-2,6-dimethyl-3-nitro-4-(3-trifluoromethylphenyl)-pyridine-5-carboxylate], and Bay O 9507 [methyl 1,4-dihydro-2,6-dimethyl-3-nitro-4-(4-nitrophenyl)-pyridine-5-carboxylate] were determined. The conformations of the 1,4-DHP rings of these activator analogues of Bay K 8644 [methyl 1,4-dihydro-2,6-dimethyl-3-nitro-4-(2-trifluoromethylphenyl)-pyridine-5- carboxylate] do not suggest that their activator properties are as strongly correlated with the degree of 1,4-DHP ring flattening as was indicated for members of the corresponding antagonist series. The solid state hydrogen bonding of the N(1)-H groups of the activators is not, unlike that of their antagonist counterparts, to acceptors that are directly in line with the donor. Rather, acceptor groups are positioned within ± 60 degrees of the N(1)-H bond in the vertical plane of the 1,4-DHP ring. Previously determined structure-activity relationships have indicated the importance of this N(1)-H group to the activity of the 1,4-DHP antagonists. Based on these observations, a model is advanced to describe the 1,4-DHP binding site of the voltage-gated Ca²⁺ channel and its ability to accommodate both antagonist and activator ligands.     

Comparative molecular modelling study of the calcium channel blockers nifedipine and black mamba toxin FS2

The identification and structural determination of the criticalamino acid residues causing the calcium channel blocking effects of theangusticeps type III toxin FS₂ is described. Alignments withmore than 200 different short and long neuro-, cyto-, muscarinic and otherangusticeps-type toxins yielded 12 amino acid residues at the tips of loopsII and III which are unique to the type III toxins. The competitive bindingbehaviour between the 1,4-dihydropyridine derivative nifedipine and toxinFS₂ was used for a further delimitation of the relevant toxinbinding domain. Using the ab initio geometry optimized nifedipine X-raystructure as a template, a model based on the sequenceMet⁴⁵-Trp⁴⁶-cis-Pro⁴⁷-Tyr⁴⁸has been elaborated. This sequence shows the same hydrophobic andhydrogen bond forming properties as nifedipine. In addition, qualitativelysimilar molecular electrostatic potentials are observed for both structures,leading to the assumption that these amino acid residues of the toxin act asthe potential attachment region at the calcium channel receptor site.     

Conformational flexibility of the 1,4-dihydropyridine ring in calcium channel agonists and antagonists molecules

Conformational flexibility of the 1,4-dihydropyridine ring in 4-aryl derivatives of the 2,6-dimethyl-3,5-dicarbmethoxy-1,4-dihydropyridine has been studied using the MM3 molecular mechanics method. Change of the C=C---C---C= endocyclic torsion angle of dihydrocycle in the range of 35° entails an increase of energy less than 1 kcal mol⁻¹. The energy levels below 99% of the molecular population for each molecule were estimated. The interval of the torsion angle change for these regions is about 60°.     

Micellar electrokinetic chromatography as a fast screening method for the determination of 1,4-dihydropyridine calcium antagonists

A micellar electrokinetic chromatographic method (MEKC) was optimized for the separation of six calcium antagonists. The effects of the buffer (concentration and pH), concentration of sodium dodecyl sulphate (SDS), the organic modifier, the injection time, and the voltage applied were studied. A final appropriate electrolyte of 50 mM borate buffer, pH 8.2, containing 20 mM SDS and 15% (v/v) acetonitrile was found to provide the optimum separation with respect to resolution and migration time. The samples were introduced hydrostatically for 4 s at 50 mbar injection pressure and the applied voltage was +25 kV. The screening of the six compounds was achieved in less than 15 min: nifedipine (migration time, tm = 6.9 min), nimodipine (tm = 10.1 min), felodipine (tm = 12.2 min), nicardipine hydrochloride (tm = 12.7 min), lacidipine (tm = 13.5 min) and amlodipine besylate (tm = 14.1 min, tm = 8 min). The method developed showed to be linear at least up to 70 micrograms/ml with a detection limit of about 5 micrograms/ml for each compound. The within-day and inter-day area reproducibility (R.S.D.) were, respectively, lower than 4.8 and 8.6% for six replicate samples.     

Improvement of the chromatographic separation of several 1,4-dihydropyridines calcium channel antagonist drugs by experimental design

A high-performance liquid chromatographic method with diode array detection has been developed and optimized for the separation of five calcium channel blockers belonging to the 1,4-dihydropyridine subgroup (nifedipine and related drugs). The possibility of the simultaneous drug analysis allows a decrease of time during the assay as well as a saving of reagents and solvents. In this work, the effect of four experimental parameters (organic modifier percentage, pH value, concentration of the buffer in the mobile phase, and column temperature) on the chromatographic resolution are investigated by experimental design in order to optimize the chromatographic separation of five 1,4-dihydropyridines (amlodipine, nitrendipine, felodipine, lacidipine, and lercanidipine). Fractional factorial design, central composite design, and finally the Multisimplex program are used to establish the optimal conditions in terms of resolution and minimum analysis time. Optimal separation of the five compounds under study is achieved in less than 12 min using a Sulpecosil LC-ABZ+Plus C18 column, a composition of mobile phase of acetonitrile-10mM acetic acid acetate buffer pH 5 (72:28, v/v) at a flow rate of 1 mL/min, a column temperature of 30 degrees C +/- 0.1 degrees C, and a detection wavelength of 238 nm.     

Oxidation of cationic 1,4-dihydropyridine derivatives as model compounds for putative gene delivery agents

A new synthetic approach to cationic pyridine derivatives is described here. Two different strategies for the synthesis of 1,1′-{[3,5-bis(ethoxycarbonyl)-4-phenylpyridine-2,6-diyl]dimethylene}bispyridinium salts have been developed. The key step of the first strategy relies on electrochemical and chemical oxidation of cationic 1,4-dihydropyridines; the second one involves nucleophilic substitution of pyridine dibromo derivatives.     

Synthesis and studies of calcium channel blocking and antioxidant activities of novel 4-pyridinium and/or N-propargyl substituted 1,4-dihydropyridine derivatives

The novel 1,4-dihydropyridine derivatives containing the cationic pyridine moiety at the position 4, and the N-propargyl group as a substituent at position 1 of the 1,4-DHP cycle were designed, synthesised, and assessed in biological tests. Among all the novel compounds, the 4-(N-dodecyl) pyridinium group-containing compounds 11 (without the N-propargyl group) and 12 (with the N-propargyl group) demonstrated the highest calcium antagonistic properties against neuroblastoma SH-SY5Y (IC₅₀ about 5–14 μM) and the vascular smooth muscle A7r5 cell (IC₅₀ – 0.6–0.7 μM) lines, indicating that they predominantly target the L-type calcium channels. These compounds showed a slight total antioxidant activity. At concentrations close to those of L-type calcium channel blocking ones, compound 12 did not affect mitochondrial functioning; also, no toxicity was obtained in vivo. The N-propargyl group as a substituent at position 1 of the 1,4-DHP cycle did not essentially influence the compounds’ activity. The 4-(N-dodecyl) pyridinium moiety-containing compounds can be considered as prototype molecules for further chemical modifications and studies as cardioprotective/neuroprotective agents.     

A molecular mechanics study of the selectivity of crown ethers for metal ions on the basis of their size

A molecular mechanics (MM) analysis is carried out on complexes of crown ethers CH₂(OCH₂CH₂)_nCH₂O, 12-crown-4 (n=3), 15-crown-5 (n=4), 18-crown-6 (n=5), 24-crown-8 (n=7), and 30-crown-11 (n=9) to determine the nature of the selectivity shown by these ligands for metal ions on the basis of metal ion size. The MM program used is SYBYL, and M-O bonds are represented using a covalent model, i.e. the M-O bonds are modelled with ideal M-O bond lengths and force constants. The previously used technique of calculating strain energy as a function of M-O bond length is used for all the complexes, and also the complexes of the non-macrocyclic polyethylene glycol analogues. It is concluded that the crown ethers fall into three groups with regard to selectivity for metal ions. Group one consists of the smaller macrocycles such as 12-crown-4 and 15-crown-5, where metal ions generally are too large to enter the cavity of the macrocycle, and the metal ion is coordinated lying outside the plane of the donor atoms of the ligand. Here factors that control selectivity are the same as in non-macrocyclic ligands, chiefly the size of the chelate ring. Group 2 contains only 18-crown-6 of the ligands studied here. 18-Crown-6 complexes have three important conformers, one of which, theD _3d , shows sharp size match selectivity, preferring metal ions with M-O bond lengths of about 2.9 . The other two conformers are adopted by metal ions too small for theD _3d conformer, and are more flexible, exerting little size-match selectivity. These other two conformers are of higher energy than theD _3d conformer for metal ions with M-O bond lengths greater than 2.55 . Thus, a genuine size match selectivity is found for K⁺ with 18-crown-6. With an ideal M-O bond length of 2.88 , K⁺ fits the cavity of theD _3d conformer of 18-crown-6 very closely. The third group consists of very large macrocycles such as 24-crown-8 and 30-crown-10. These enfold the metal ion in extremely folded conformations, but may, as does 30-crown-10, exert considerable selectivity for metal ions on the basis of their size by virtue of the conformation resulting in a set of torsional angles in the ring atoms of the macrocycle which confer considerable rigidity on the ligand.     

Cu-catalyzed one-pot multicomponent approach for the synthesis of symmetric and asymmetric 1,4-dihydropyridine (1,4-DHP) linked 1,2,3-triazole derivatives

Abstract

Synthesis of various symmetric and asymmetric 1,4-DHP linked 1,2,3-triazole derivatives from economical and readily available starting materials via a convenient methodology in a single-pot method using CuSO₄·5H₂O as an efficient catalyst has been reported. The reaction proceeded efficiently under the optimized reaction conditions with excellent functional group compatibility providing the desired products in good yields. The method appears to be an efficient combinatorial strategy for the synthesis of new 1,4-DHP linked triazole derivatives.     

Novel density-based model for the correlation of solid drugs solubility in supercritical carbon dioxide

A novel density-based model derived by a simple modification of the Jouyban et al. model has been proposed to correlate the solubility of solid drugs in supercritical carbon dioxide. The six-parameter model expresses the solubility only as a function of the solvent density and the equilibrium temperature. This model is in contrast to the Jouyban et al. (J. Superiority. Fluids 24 (2002) 19) model, which gives the solubility as a function of the solvent density and the equilibrium temperature and pressure. The performance of the model has been tested on a database of 100 drugs that account for 2891 experimental data points collected from the literature. The comparison in terms of the mean absolute relative deviation for each solid drug and for the entire database between the proposed model and models that have been suggested to be mostly more accurate demonstrates that the proposed model has the best global correlation performance, exhibiting an overall average absolute relative deviation of 8.13%.     

Exploring the molecular basis of selectivity in A1 adenosine receptors agonists: a case study

Adenosine is a naturally occurring purine nucleoside that has a wide variety of well-documented regulatory functions and physiological roles. Selective activation of the adenosine A₁ receptor has drawn attention in drug discovery for the therapeutic effects on neural and cardiovascular disorders. We have developed a model of the human A₁ adenosine receptor using bovine rhodopsin as a template. A flexible docking approach has been subsequently carried out for evaluating the molecular interactions of twenty-one selective A₁ agonists with the receptor model. The results of these studies are consistent with mutational and biochemical data. In particular, they highlight a wide hydrogen-bonding network between the nucleoside portion of the ligands and the A₁ receptor as well as key amino acids for hydrophobic interactions with the different N⁶-groups of the agonists. The models presented here provide a detailed molecular map for the selective stimulation of the adenosine A₁ receptor subtype and a steady basis for the rational design of new A₁ selective ligands.     

A molecular thermodynamic model for the swelling of thermo-sensitive hydrogels

A new molecular thermodynamic model for describing the swelling behavior of thermo-sensitive hydrogels was developed. The model consists of two terms. One is the contribution of the mixing of hydrogel network and water, which is dependent on the local polymer concentration and the interaction between polymer segment and solvent. A closed packed lattice model for polymer solution developed by Yang et al. was adopted for this term. The other is the elastic contribution derived from the network elasticity, which is dependent on the cross-linking degree of gel network. The elastic Gibbs energy model based on the Gaussian chain model developed by Flory was adopted. The model equation has two parameters. One is an energy parameter ? reflecting the interaction between water and gel network, the other is a size parameter V^* that represents the cross-linking degree of the hydrogel. When the energy parameter ? is expressed as a quadratic of inverse temperature, this model can describe the swelling equilibrium behavior of neutral thermo-sensitive hydrogels quite well. The influences of model parameters were discussed in details. The experimental swelling curves of two kinds of polyacrylamide-based gels were correlated and good agreement was obtained.     

Towards an identification of the pyrethroid pharmacophore. A molecular modelling study of some pyrethroid esters

Summary A molecular modelling and computer graphics study of a series of pyrethroid insecticides has been carried out. The three-dimensional arrangement of the groups essential for the biological activity (pharmacophore) has been identified for the acid and the alcohol moieties, respectively. These pharmacophores are based on the relationship between molecular structure and biological activity for a number of pyrethroid esters. The pharmacophores, which describe the relative location in space of the unsaturated systems, the dimethyl groups and the ester moiety, may be useful in the design of novel compounds with pyrethroid activity.     

Development of a liquid-liquid extraction procedure for five 1,4-dihydropyridines calcium channel antagonists from human plasma using experimental design

A liquid–liquid extraction method using diethyl ether as organic solvent was optimized simultaneously for five 1,4-dihydropyridines (amlodipine, nitrendipine, felodipine, lacidipine and lercanidipine) belonging to the group of calcium channel blockers. Some experimental tools such as a full factorial design, a central composite design and the Multisimplex program were used to optimise the concentration of NaOH, volume of organic solvent and shaking time as main factors that influence the liquid–liquid extraction procedure. Following the extraction, the quantitation of the 1,4-dihydropyridines concentrations were performed by high-performance liquid chromatography with diode-array detector. Therefore, the studied compounds were separated quantitatively on a Supelcosil ABZ+Plus, 25 cm × 4.6 mm i.d., 5 μm column which was set at 30 °C, using as mobile phase, a mixture of acetonitrile–water (70:30, v/v) containing 10 mM acetate buffer (pH 5) and setting the detector at a wavelength value of 360 nm. It was concluded that the main factors that influence in the extraction process were the volume of organic solvent and the shaking time. The Multisimplex program suggested as optimal conditions an average of 6 ml of organic solvent and 23 min of shaking time. For these values, the optimised liquid–liquid extraction method showed good values of recoveries (80% for amlodipine and higher than 90% for the rest of the compounds) and low values of R.S.D. (<10%) in the reproducibility of the extraction what makes it reliable for the quantification of all the studied compounds in human plasma.     

Analysis of calcium blocker drugs in plasma,HRGC and HPLC analytical conditions for pharmacokinetic studies

Calcium blocker drugs are of increasing therapeutic relevance. Verapamil, nifedipine, diltiazem, and flunarizine are the most widely applied drugs of this type. New dihydropyridines (felodipine, nitrendipine) and related agents are presently undergoing intense investigation. HRGC and HPLC were used to determine eight of these drugs in spiked plasma samples. Both methods allow separation of most of the compounds in a single run and are specific, sensitive, and reproducible both for therapeutic monitoring and for pharmacokinetic studies in man and animals.     

基于药效团模型从中草药数据库中搜索gpIIb/IIIa受体抑制剂

选择20 个3,4-二氢-1(1H)-异喹啉酮类gpIIb/IIIa受体抑制剂作为训练集, 利用Catalyst软件包建立了gpIIb/IIIa受体抑制剂三维药效团模型. 探讨了药效团作用模式. 并通过建立的可靠性最佳的药效团模型(线性回归系数r=0.7715), 从中草药数据库中虚拟筛选了gpIIb/IIIa受体抑制剂, 通过实验活性测定得到了8个抑制ADP活化全血血小板聚集的IC50从40到100 μmol·L-1的化合物, 进一步证明了所建药效团模型的有效性.     

Simulation model for the molecular weight distribution in emulsion polymerization

A Monte Carlo simulation model for the kinetics of emulsion polymerization is proposed. In the present model, the formation of each polymer molecule is simulated by the use of only a couple of probability functions; therefore, the calculation can be handled well even on personal computers. It is straightforward to account for virtually any kinetic event, such as the desorption of oligomeric radicals and chain length dependence of kinetic parameters, and as a consequence very detailed information such as the full distributions of the dead polymer molecular weights and the macroradicals among various polymer particles can be obtained. When bimolecular terminations are the dominant chain stoppage mechanism, the instantaneous molecular weight distribution (produced in a very small time interval) becomes broader than that for homogeneous polymerizations due to a higher possibility that short and long polymer radicals react with each other if bimolecular reactions are fast enough. The increase in the polydispersity of the MWD is fairly large, especially when bimolecular termination by disproportionation is significant; however, the gel permeation chromatography (GPC) may not be a suitable analytical technique to detect such broadening since oligomeric peaks may not be observed in the elution curve. The present simulation method provides greater insight into the complicated phenomena of emulsion polymerizations. © 1995 John Wiley & Sons, Inc.     

Complete basis set model chemistry applied to molecules of increasing molecular complexity: Thermochemical properties of organic sulfur derivatives

To estimate the thermochemical properties, bond dissociation energies and atomization energies of sulfur organic derivatives, the complete basis set (CBS) method was employed at the lower computational level (CBS‐4) owing to the large molecular size of a number of the molecules chosen. By comparison with experimental values, calculated values of thermochemical properties are subject to error, which increases in line with the increase in molecular complexity. The main source of error affecting the calculated enthalpy of formation stems from the difference between the energy of the molecule and that of the single atoms: the greater the size of the molecule, the greater the accumulation of error. By acting on the empirical correction to the CBS energy and minimizing the error due to the contribution of the single atoms to the dissociation energy a parameter d_i for each atom i is obtained. Application of these corrections does not greatly affect the heats of formation of the small molecules included in test sets employed for previous comparisons of calculated and experimental values, while there is a great improvement in the case of large molecules, for example, diphenyl disulfide. The mean absolute deviation turns out to be 2.52, which is greater than that obtained in recent reexaminations of model chemistry methods including the G3 and G3(MP3) approaches. The improvement in the results calculated for large molecules, whose heats of formation are calculated with large errors at the CBS‐4 level, in comparison also with the CBS‐4M version, justify our approach. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1405–1418, 2000