Reliable structural information for rational design of benzoxazole type potential cholesteryl ester transfer protein (CETP) inhibitors through multiple validated modeling techniques

Abstract

The drug design and discovery of lipid modulators is very demanding as no new molecule has entered into the market in the last 35 years. Cholesteryl ester transfer protein (CETP) is a promising target as lipid modulators. Inhibition of the CETP enzyme reduces the risk of cardiovascular events. The first CETP inhibitor torcetrapib and related drug candidates failed in the clinical trial due to the off-target effects leading to high toxicity. Thus, newer CETP inhibitors have now paramount importance to accelerate the drug discovery efforts in the field of cardiovascular disease (CVD). In the present study, 140 benzoxazole compounds were studied by using different chemometric techniques, for example, pharmacophore mapping, molecular docking, three-dimensional quantitative structure–activity relationship comparative molecular field analysis (3D-QSAR CoMFA), topomer CoMFA and Bayesian classification, in order to generate complete and reliable information regarding the structural requirements for the CETP inhibition. The best pharmacophore hypothesis was statistically significant (regression coefficient of 0.957 and a lower root mean square of 0.890). Molecular docking study revealed that cyano-substituted compounds form hydrogen bond with targeted macromolecule. The 3D-QSAR CoMFA model also produced a leave-one-out (LOO) cross-validated Q² of 0.527, an R² of 0.853 and an R²_Pred of 0.603. Similarly, two topomer CoMFA models were also statistically significant and reliable in terms of their Q², R² and R²_Pred values. The Bayesian classification study also provided the excellent ROC values of 0.919 and 0.939 for training and test sets, respectively. Overall, this study may help in the rational design of newer benzoxazole type compounds with higher CETP inhibition.

Communicated by Ramaswamy H. Sarma     

Studies of H4R antagonists using 3D-QSAR,molecular docking and molecular dynamics

Three-dimensional quantitative structure–activity relationship studies were performed on a series of 88 histamine receptor 4 (H4R) antagonists in an attempt to elucidate the 3D structural features required for activity. Several in silico modeling approaches, including comparative molecular field analysis (CoMFA), comparative similarity indices analysis (CoMSIA), molecular docking, and molecular dynamics (MD), were carried out. The results show that both the ligand-based CoMFA model (Q ² = 0.548, R _ncv² = 0.870, R _pre² = 0.879, SEE = 0.410, SEP = 0.386) and the CoMSIA model (Q ² = 0.526, R _ncv² =0.866, R _pre² = 0.848, SEE = 0.416, SEP = 0.413) are acceptable, as they show good predictive capabilities. Furthermore, a combined analysis incorporating CoMFA, CoMSIA contour maps and MD results shows that (1) compounds with bulky or hydrophobic substituents at positions 4–6 in ring A (R2 substituent), positively charged or hydrogen-bonding (HB) donor groups in the R1 substituent, and hydrophilic or HB acceptor groups in ring C show enhanced biological activities, and (2) the key amino acids in the binding pocket are TRP67, LEU71, ASP94, TYR95, PHE263 and GLN266. To our best knowledge, this work is the first to report the 3D-QSAR modeling of these H4R antagonists. The conclusions of this work may lead to a better understanding of the mechanism of antagonism and aid in the design of new, more potent H4R antagonists.     

Evaluation of (Z)-2-((1-benzyl-1H-indol-3-yl)methylene)-quinuclidin-3-one analogues as novel,high affinity ligands for CB1 and CB2 cannabinoid receptors

A small library of N-benzyl indolequinuclidinone (IQD) analogs has been identified as a novel class of cannabinoid ligands. The affinity and selectivity of these IQDs for the two established cannabinoid receptor subtypes, CB1 and CB2, was evaluated. Compounds 8 (R = R² = H, R¹ = F) and 13 (R = COOCH₃, R¹ = R² = H) exhibited high affinity for CB2 receptors with K_i values of 1.33 and 2.50 nM, respectively, and had lower affinities for the CB1 receptor (K_i values of 9.23 and 85.7 nM, respectively). Compound 13 had the highest selectivity of all the compounds examined, and represents a potent cannabinoid ligand with 34-times greater selectivity for CB2R over CB1R. These findings are significant for future drug development, given recent reports demonstrating beneficial use of cannabinoid ligands in a wide variety of human disease states including drug abuse, depression, schizophrenia, inflammation, chronic pain, obesity, osteoporosis and cancer.     

Use of molecular modeling, docking, and 3D-QSAR studies for the determination of the binding mode of benzofuran-3-yl-(indol-3-yl)maleimides as GSK-3β inhibitors

Molecular modeling and docking studies along with three-dimensional quantitative structure relationships (3D-QSAR) studies have been used to determine the correct binding mode of glycogen synthase kinase 3β (GSK-3β) inhibitors. The approaches of comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) are used for the 3D-QSAR of 51 substituted benzofuran-3-yl-(indol-3-yl)maleimides as GSK-3β inhibitors. Two binding modes of the inhibitors to the binding site of GSK-3β are investigated. The binding mode 1 yielded better 3D-QSAR correlations using both CoMFA and CoMSIA methodologies. The three-component CoMFA model from the steric and electrostatic fields for the experimentally determined pIC₅₀ values has the following statistics: R²(cv) = 0.386 nd SE(cv) = 0.854 for the cross-validation, and R² = 0.811 and SE = 0.474 for the fitted correlation. F (3,47) = 67.034, and probability of R² = 0 (3,47) = 0.000. The binding mode suggested by the results of this study is consistent with the preliminary results of X-ray crystal structures of inhibitor-bound GSK-3β. The 3D-QSAR models were used for the estimation of the inhibitory potency of two additional compounds.     

Synthesis and characterization of silver(I) derivatives containing acylpyrazolonate and phosphino ligands: X-ray crystal structures of monomeric [Ag(Q)(PPh3)2] and of dimeric [{Ag(Q)(PiBu3)}2] (Q = 1-phenyl-3-methyl-4-tert-butylacetylpyrazolon-5-ato)

New silver(I) acylpyrazolonate derivatives [Ag(Q)], [Ag(Q)(PR₃)]₂ and [Ag(Q)(PR₃)₂] (HQ = 1-R¹-3-methyl-4-R²(CO)pyrazol-5-one, HQ^Bn = R¹ = C₆H₅, R² = CH₂C₆H₅; HQ^CHPh2 = R¹ = C₆H₅, R² = CH(C₆H₅)₂; HQ^nPe = R¹ = C₆H₅, R² = CH₂C(CH₃)₃; HQ^tBu = R¹ = C₆H₅, R² = C(CH₃)₃; HQ^fMe = R¹ = C₆H₄-p-CF₃, R² = CF₃; HQ^fEt = R¹ = C₆H₅, R² = CF₂CF₃; R = Ph or iBu) have been synthesized and characterized in the solid state and solution. The crystal structure of 1-(4-trifluoromethylphenyl)-3-methyl-5-pyrazolone, the precursor of proligand HQ^fMe and of derivatives [Ag(Q^nPe)(PPh₃)₂] and [Ag(Q^nPe)(PiBu₃)]₂ have been investigated. [Ag(Q^nPe)(PPh₃)₂] is a mononuclear compound with a silver atom in a tetrahedrally distorted AgO₂P₂ environment, whereas [Ag(Q^nPe)(PiBu₃)]₂ is a dinuclear compound with two O₂N-exotridentate bridging acylpyrazolonate ligands connecting both silver atoms, their coordination environment being completed by a phosphine ligand.     

Comparative molecular field analysis of fenoterol derivatives interacting with an agonist-stabilized form of the β2-adrenergic receptor

The β₂-adrenergic receptor (β₂-AR) agonist [³H]-(R,R′)-methoxyfenoterol was employed as the marker ligand in displacement studies measuring the binding affinities (K_i values) of the stereoisomers of a series of 4′-methoxyfenoterol analogs in which the length of the alkyl substituent at α′ position was varied from 0 to 3 carbon atoms. The binding affinities of the compounds were additionally determined using the inverse agonist [³H]-CGP-12177 as the marker ligand and the ability of the compounds to stimulate cAMP accumulation, measured as EC₅₀ values, were determined in HEK293 cells expressing the β₂-AR. The data indicate that the highest binding affinities and functional activities were produced by methyl and ethyl substituents at the α′ position. The results also indicate that the K_i values obtained using [³H]-(R,R′)-methoxyfenoterol as the marker ligand modeled the EC₅₀ values obtained from cAMP stimulation better than the data obtained using [³H]-CGP-12177 as the marker ligand. The data from this study was combined with data from previous studies and processed using the Comparative Molecular Field Analysis approach to produce a CoMFA model reflecting the binding to the β₂-AR conformation probed by [³H]-(R,R′)-4′-methoxyfenoterol. The CoMFA model of the agonist-stabilized β₂-AR suggests that the binding of the fenoterol analogs to an agonist-stabilized conformation of the β₂-AR is governed to a greater extend by steric effects than binding to the [³H]-CGP-12177-stabilized conformation(s) in which electrostatic interactions play a more predominate role.     

Barium acylpyrazolonate derivatives stabilized by O- and N-donor ligands: synthesis, spectral and structural characterization

New Ba acylpyrazolonate derivatives of formula [Ba(Q)₂(tetraglyme)] (HQ = HQ^tbu = 1-Ph-3-Me-4-C(O)CH₂Bu^t-5-pyrazolone; tetraglyme = 2,5,8,11,14-pentaoxapentadecane), [Ba(Q)₂(tmeda)₂] (HQ = HQ^tbu or HQ^piv, where HQ^piv = 1-Ph-3-Me-4-C(O)Bu^t-5-pyrazolone; tmeda = N,N,N′,N′-tetramethylethylenediamine), [Ba(Q)₂(pmdien)(H₂O)] (HQ = HQ^tbu or HQ^piv; pmdien = N,N,N′,N″,N″-pentamethyldiethylenetriamine) and [Ba(Q)₂(pmdien)(Meim)] (HQ = HQ^tbu or HQ^piv; Meim = 1-methylimidazole) have been synthesized and analytically and spectroscopically characterized. They are mononuclear air and solution stable compounds containing an eight-coordinated barium atom. The X-ray crystal structures of the hydrates [Ba(Q^tbu)₂(pmdien)(H₂O)] and [Ba(Q^piv)₂(pmdien)(H₂O)] show the water molecule directly bonded to Ba and involved in intermolecular H-bonding network. In the X-ray crystal structure of [Ba(Q^piv)₂(pmdien)(Meim)], the Meim ligand substitutes the water of previous derivatives and decreases the strength of intermolecular interactions, lowering the melting point. The derivative [Ba(Q^tbu)₂(pmdien)(NEt₃)] has been prepared from interaction of [Ba(Q^tbu)₂(pmdien)(H₂O)] with excess triethylamine in acetonitrile.     

Hybrid scorpionate/cyclopentadienyl titanium and zirconium complexes with alkoxide and imido ligands

The reactivity of hybrid scorpionate/cyclopentadienyl ligand-containing trichloride zirconium complexes [ZrCl₃(bpzcp)] (1) [bpzcp = 2,2-bis(3,5-dimethylpyrazol-1-yl)-1,1-diphenylethylcyclopentadienyl] and [ZrCl₃(bpztcp)] (2) [bpztcp = 2,2-bis(3,5-dimethylpyrazol-1-yl)-1-tert-butylethylcyclopentadienyl] toward several lithium alkoxides has been carried out. Thus, alkoxide-containing complexes [ZrCl₂(OR)(bpzcp)] (R = Me, 3; Et, 4; ⁱPr, 5; (R)-2-Bu, 6), [ZrCl₂(OR)(bpztcp)] (R = Me, 7; Et, 8; ⁱPr, 9; (R)-2-Bu, 10) and [Zr(OR)₃(bpztcp)] (R = Et, 11; ⁱPr, 12) were prepared by deprotonation of the appropriate alcohol group with BuⁿLi followed by reaction with 1 or 2. In addition, the imido-complex [Ti(N^tBu)Cl(bpztcp)(py)] (13) were also prepared. The structures of these complexes have been proposed on basis of spectroscopic and DFT methods.     

Silver(I) derivatives with new functionalised acylpyrazolonates

Silver(I) acylpyrazolonate derivatives of formula [Ag(Q)(R₃P)]₂ and [Ag(Q)(R₃P)₂], (QH=1-phenyl-3-methyl-4-R′(CO)-pyrazol-5-one; Q^OH, R′=furane; Q^SH, R′=thiophene; R=Ph, Cy, o-tol), have been synthesised and characterised, both in the solid state and in solution. The derivatives [Ag(Q)(R₃P)]₂ contain dinuclear AgO₂NP units with the acylpyrazolonate coordinating in a bridging O,O′-Q-N fashion. The [Ag(Q)(R₃P)₂] are tetrahedral species, with the distortion from ideal geometry increasing with the bulk of the phosphine. The [Ag(Q)(R₃P)₂] derivatives are fluxional in chloroform solution when R₃P is sterically hindered (R=Cy or o-tol), dissociating partially to the [Ag(Q)(R₃P)] fragment and free R₃P. [Ag(Q^S)(Ph₃P)]₂ reacts with 1-methyl-2-mercaptoimidazole (Hmimt) affording the compound [Ag(Hmimt)(Ph₃P)(Q^S)] and [Ag(Q^O)(Ph₃P)]₂ reacts with 1-methyl-imidazole (Meim) affording the compound [Ag(Meim)(Ph₃P)(Q^O)], whereas [Ag(Q^S)(Ph₃P)]₂ reacts with 1,10-phenanthroline (phen), affording the compound [Ag(phen)(Ph₃P)](Q^S). Finally [Ag(Q^S)(Ph₃P)₂] reacts with phen producing the ionic species [Ag(phen)(Ph₃P)₂](Q^S).     

The rate of convergence of a generalized stable population

In an age-structured population that grows exponentially, each age groupP _i(t) at periodt is asymptotically equivalent tox ₀ ^t for some positive number x₀. In this paper we show that the speed at which the ith age group reaches its exponential state of equilibrium can be measured by the rate at which the ratio v_i(t)=P_i(t)/p_i(t–1) converges tox ₀. The age specific rate of convergence is determined by considering a quantityr satisfyingv _i(t)-x ₀ ¦ r ^t whent is large;R _i=Infr (over all initial populations,r satisfying the above inequality) is the R-factor used in numerical analysis to measure the rate at which the sequencev _i (t) converges tox ₀;S _i =- In R_i is then defined as the rate of convergence to stability of the ith age group. The case of constant net maternity rates is studied in detail; in this contextS ₀ is compared to the population entropyH, which was proposed by Tuljapurkar (1982) as a measure of the rate of convergence to stability.     

Characterisation of [3H]-Darifenacin as a Novel Radioligand for the Study of Muscarinic M3 Receptors

Abstract

Darifenacin, (S)-2-[1-[2,3-dihydrobenzofuran-5-yl]-3-pyrrolidinyl]-2,2-diphenylacetamide, is a novel muscarinic M₃ antagonist. In this study we have compared the binding of [³H]-darifenacin to the five cloned human muscarinic receptors (m₁ - m₅) expressed in CHO cells. [³H]-darifenacin binds with 6 fold higher affinity to m₃ (K_D = 0.33 nmol/l) over m₁ (K_D = 1.6 nmol/l) receptors. There was no specific binding of [³H]-darifenacin to m₂ receptors and specific binding to m₄ and m₅ receptors was insufficient to determine a K_D. Binding of [³H]-darifenacin to m₁ and m₃ was displaced by atropine (m₁ pK_i = 9.36, m₃ pK_i = 9.4), 4-DAMP (m₁ pK_i = 9.04, m₃ pK_i = 9.19), pirenzepine (m₁ pK_i = 8.63, m₃ pK_i = 6.85), methoctramine (m₁ pK_i = 7.28, m₃ pK_i = 6.63), and darifenacin (m₁ pK_i = 8.36, m₃ pK_i = 9.14), demonstrating that [³H]-darifenacin represents the first selective m₃ radioligand.     

CoMFA and CoMSIA analyses on 1,2,3,4-tetrahydropyrrolo[3,4-b]indole and benzimidazole derivatives as selective CB2 receptor agonists

Novel classes of cannabinoid 2 receptor (CB2) agonists based on 1,2,3,4-tetrahydropyrrolo[3,4-b]indole and benzimidazole scaffolds have shown high binding affinity toward CB2 receptor and good selectivity over cannabinoid 1 receptor (CB1). A computational study of comparative molecular fields analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) was performed, initially on each series of agonists, and subsequently on all compounds together, in order to identify the key structural features impacting their binding affinity. The final CoMSIA model resulted to be the more predictive, showing cross-validated r² (r_cv ²) = 0.680, non cross-validated r² (r_ncv ²) = 0.97 and test set r²( r_pred² ) = 0.93 {{\hbox{r}}^2}\left( {{\hbox{r}}_{\rm{pred}}^2} \right) = 0.{93} . The study provides useful suggestions for the design of new analogues with improved affinity.     

Inhibition of an outwardly rectifying anion channel by HEPES and related buffers

Summary The effect of pH buffers and related compounds on the conductance of an outwardly rectifying anion channel has been studies using the patch-clamp technique. Single-channel current-voltage relationships were determined in solutions buffered by trace amounts of bicarbonate and in solutions containing N-substituted taurines (HEPES, MES, BES, TES) and glycines (glycylglycine, bicine and tricine), Tris andbis-Tris at millimolar concentrations. HEPES (pK_a=7.55) reduced the conductance of the channel when present on either side of the membrane. Significant inhibition was observed with 0.6mm HEPES on the cytoplasmic side (HEPES _i ) and this effect increased with [HEPES _i ] so that conductance at the reversal potential was diminished 25% with 10mm HEPES _i )and 70% at very high [HEPES _i ]. HEPES _i block was relieved by applying positive voltage but positive currents were not consistent with a Woodhulltype blocking scheme in that calculated dissociation constants and electrical distances depended on HEPES concentration. Results obtained by varying total HEPES _i concentration at constant [HEPES^–] and vice versa suggest both the anionic and zwitterionic (protonated) forms of HEPES inhibit. Structure-activity studies with related compounds indicate the sulfonate group and heterocyclic aliphatic groups are both required for inhibition from the cytoplasmic side. TES (pK_a=7.54), substituted glycine buffers (pK_a=8.1–8.4) andbis-Tris (pK_a=6.46) had no measurable effect on conductance and appear suitable for use with this channel.     

Understanding DP receptor antagonism using a CoMSIA approach

A Comparative Molecular Similarity Indices Analysis (CoMSIA) was performed for 2,6-substituted-4-monosubstituted aminopyrimidine antagonists of prostaglandin D₂ receptor (DP). Both two-component (Q² = 0.63, R² = 0.82, SEE = 0.47 pIC₅₀) and three-component (Q² = 0.70, R² = 0.91, SEE = 0.36 pIC₅₀) CoMSIA models were established. Two hydrogen-bond acceptors with spatial separation of about 8 Å are shown as optimal for binding. A large hydrophobic center that separates the two acceptors confers to the potency of the 2,6-substituted-4-monosubstituted aminopyrimidine. The models were used to predict IC₅₀ values for compounds which had functional groups different from those in the training set.     

Bis(phosphine)-Pd(II) and -Pt(II) complexes containing chiral tetrazole-thiolato rings: Synthesis, structures, and reactivity toward some electrophiles

Bis(azido)bis(phosphine)-Pd(II) and -Pt(II) complexes, [M(N₃)₂L₂] {L = PMe₃, PEt₃, PMe₂Ph, dppe = 1,2-bis(diphenylphosphino)ethane}, underwent 1,3-dipolar cycloaddition with organic chiral isothiocyanates (R^∗-NCS: R^∗ = (S)-(+)-1-phenylethyl, (R)-(−)-1-phenylethyl, (±)-1-phenylethyl, (S)-(+)-1-indanyl) to give the corresponding tetrazole-thiolato Pd(II) and Pt(II) complexes, trans-[M{S[CN₄(R^∗)]}₂L₂] or [M{S[CN₄(R^∗)]}₂(dppe)]. Spectroscopic (IR and NMR) and X-ray structural analyses of the products showed that the absolute configuration of the starting organic isothiocyanates is retained throughout the reaction. Further treatments of the isolated tetrazole-thiolato complexes with electrophiles such as HCl or benzoyl chloride produced heterocyclic compounds containing a tetrazole thione or a tetrazolyl sulfide group. In addition, organic tetrazole thiones, [S = {CN₄H(R^∗)}] containing a chiral moiety, were prepared from NaN₃ and R^∗-NCS in the presence of water.