3D-QSAR CoMFA study on imidazolinergic I(2) ligands: a significant model through a combined exploration of structural diversity and methodology

Clustering of atoms relative to vector space in the Z-matrix coordinate system and 'graphical fingerprint' analysis of 3D pharmacophore structure

The behavior of a molecule within its environment is governed by chemical fields present in 3D space. However, beyond local descriptors in 3D, the conformations a molecule assumes, and the resulting clusters also play a role in influencing structure-activity models. This study focuses on the clustering of atoms according to the vector space of four atoms aligned in the Z-Matrix Reference system for molecular similarity. Using 3D-QSAR analysis, it was aimed to determine the pharmacophore groups as interaction points in the binding region of the β2-adrenoceptor target of fenoterol stereoisomers. Different types of local reactive descriptors of ligands have been used to elucidate points of interaction with the target. Activity values for ligand-receptor interaction energy were determined using the Levenberg-Marquardt algorithm. Using the Molecular Comparative Electron Topology method, the 3D pharmacophore model (3D-PhaM) was obtained after aligning and superimposing the molecules and was further validated by the molecular docking method. Best guesses were calculated with a non-output validation (LOO-CV) method. Finally, the data were calculated using the 'graphic fingerprint' technique. Based on the eLKlopman (Electrostatic LUMO Klopman) descriptor, the Q2 value of this derivative set was calculated as 0.981 and the R2ext value is calculated as 0.998.

Diarylquinolines, synthesis pathways and quantitative structure--activity relationship studies leading to the discovery of TMC207

The emergence of multidrug-resistant strains of Mycobacterium tuberculosis and resistance to current anti-TB drugs call for the discovery and development of new effective anti-TB drugs. TMC207 is the lead candidate of a novel class of antimycobacterial agents, the diarylquinolines, which specifically inhibit mycobacterial ATP synthase and displays high activity against both drug-susceptible and multidrug-resistant strains of Mycobacterium tuberculosis. This article covers both synthesis pathways as well as qualitative and quantitative analyses of the structure-activity relationships of the diarylquinoline series on Mycobacterium smegmatis activity.

Self-organizing molecular field analysis on pregnane derivatives as human steroidal 5alpha-reductase inhibitors

Normal growth and development of human prostate is regulated by the androgens which balances cell proliferation and apoptosis. Testosterone (T) and dihydrotestosterone (DHT) are the two key androgens that stimulate most of the androgen action in prostate. Testosterone is converted to DHT by the membrane bound NADPH-dependent 5alpha-reductase enzyme. As a consequence of the important observation that progesterone and deoxycortisone inhibits the synthesis of DHT by competing with 4-en-3-one function of the testosterone for the 5alpha-reductase enzyme a number of pregnane derivatives were synthesized and have been reported as inhibitors of human 5alpha-reductase enzyme. Due to lack of information on the crystal structure of human 5alpha-reductase, ligand-based 3D-QSAR study has been performed on pregnane derivatives using self-organizing molecular field analysis (SOMFA) for rationalizing the molecular properties and human 5alpha-reductase inhibitory activities. The statistical results having good cross-validated r(cv)(2) (0.881), non-cross-validated r(2) (0.893) and F-test value (175.527), showed satisfied predictive ability r(pred)(2) (0.777). Analysis of SOMFA models through electrostatic and shape grids provide useful information for the design and optimization of steroidal structure as novel human 5alpha-reductase inhibitors.

Comparative molecular field analysis of benzothiazepine derivatives: mitochondrial sodium calcium exchange inhibitors as antidiabetic agents

Mitochondrial sodium calcium exchange inhibitors are novel agents in the treatment of type-II diabetes due to their glucose dependent efficacy. While the compounds of this class are expected to correct hyperglycemia, they do not lower basal blood glucose level, thus avoiding the serious consequences of hypoglycemia. The 3DQSAR analysis of benzothiazepines and their derivatives as mitochondrial sodium calcium exchange inhibitors was performed by comparative molecular field analysis to determine the structural factors required for the activity of these compounds. After performing a leave one out cross validation study, satisfactory results were obtained, with cross-validated q(2) and conventional r(2) values of 0.711 and 0.970, respectively. The results provided the tools for predicting the affinity of the related compounds, and guidance for the designing and synthesis of novel and potent mitochondrial sodium calcium exchange inhibitors as antidiabetic agents.

Localization of ligand binding site in proteins identified in silico

Knowledge-based models for protein folding assume that the early-stage structural form of a polypeptide is determined by the backbone conformation, followed by hydrophobic collapse. Side chain-side chain interactions, mostly of hydrophobic character, lead to the formation of the hydrophobic core, which seems to stabilize the structure of the protein in its natural environment. The fuzzy-oil-drop model is employed to represent the idealized hydrophobicity distribution in the protein molecule. Comparing it with the one empirically observed in the protein molecule reveals that they are not in agreement. It is shown in this study that the irregularity of hydrophobic distributions is aim-oriented. The character and strength of these irregularities in the organization of the hydrophobic core point to the specificity of a particular protein's structure/function. When the location of these irregularities is determined versus the idealized fuzzy-oil-drop, function-related areas in the protein molecule can be identified. The presented model can also be used to identify ways in which protein-protein complexes can possibly be created. Active sites can be predicted for any protein structure according to the presented model with the free prediction server at http://www.bioinformatics.cm-uj.krakow.pl/activesite. The implication based on the model presented in this work suggests the necessity of active presence of ligand during the protein folding process simulation.

3D-QSAR study on heterocyclic topoisomerase II inhibitors using CoMSIA

Selective topoisomerase II (Topo II) inhibitors have interested to a great extent for the design of new antitumoral compounds in recent years. Comparative molecular similarity indices analysis (CoMSIA) was performed on a series of previously synthesized benzoxazole, benzimidazole, and oxazolo(4,5-b)pyridine derivatives as eukaryotic Topo II inhibitors. A training set of 16 heterocyclic compounds was used to establish the CoMSIA model. They were constructed and geometrically optimized using SYBYL v7.0. The predictive ability of the model was assessed using a test set of 7 compounds. The best model has demonstrated a good fit having r2 value of 0.968 and cross-validated coefficient q2 value as 0.562 including steric and hydrophobic fields. The hydrophobic interactions showed a dominant role for increasing Topo II inhibitor activity and hydrophilic substituent was found more important than hydrophobic one on the 5 or 6 position of benzazole moiety. The model obtained from the present study can be useful for the modification and/or evaluation of the development of new Topo II inhibitors as potential antitumor compounds.

Determinants of volatile general anesthetic potency: a preliminary three-dimensional pharmacophore for halogenated anesthetics

We investigated the molecular basis for the immobilizing activity of halogenated volatile anesthetics using comparative molecular field analysis. In vivo potency data (expressed as minimum alveolar concentrations) for 69 structurally diverse anesthetics were obtained from the literature. The drugs were randomly divided into a training set (n = 52) used to derive the activity model and a test set (n = 17) used to independently assess the model's predictive power. The anesthetic structures were aligned so as to maximize their similarity in molecular shape and electrostatic potential to the most potent drug in the group, CF2H-(CF2)3-CH2OH. The conformers and alignments of the anesthetics with maximum similarity (calculated as Carbo indices) were retained and used to derive the comparative molecular field analysis models. The final model explained 94.2% of the variance in the observed activities of the training set compounds. The model showed good predictive capability for both the training set (cross-validated r2 = 0.705) and randomly excluded test set anesthetics (r2 = 0.837). Three-dimensional pharmacophoric maps were derived to identify the spatial distribution of key areas where steric and electrostatic interactions are important in determining immobilizing activity of the halogenated drugs and were compared with our previously published maps obtained for nonhalogenated volatile anesthetics.

Quantitative structure-activity relationship models for prediction of the toxicity of polybrominated diphenyl ether congeners

Levels of polybrominated diphenyl ethers (PBDEs) are increasing in the environment and may cause long-term health problems in humans. The similarity in the chemical structures of PBDEs and other halogenated aromatic pollutants hints on the possibility that they might share similar toxicological effects. In this work, three-dimensional quantitative structure activity relationships (3-D-QSAR) models, using comparative molecular field analysis (CoMFA) and comparative similarity indices analysis (CoMSIA), were built based on calculated structural indices and a reported experimental toxicology index (aryl hydrocarbon receptor relative binding affinities, RBA) of 18 PBDEs congeners, to determine the factors required for the RBA of these PBDEs. After performing leave-one-out cross-validation, satisfactory results were obtained with cross-validation O2 and R2 values of 0.580 and 0.995 by the CoMFA model and 0.680 and 0.982 by the CoMSIA model, respectively. The results showed clearly that the nonplanar conformations of PBDEs result in the lowest energy level and that the electrostatic index was the main factor reflecting the RBA of PBDEs. The two QSAR models were then used to predict the RBA value of 46 PBDEs for which experimental values are unavailable at present.

3D QSAR studies on antimalarial alkoxylated and hydroxylated chalcones by CoMFA and CoMSIA

The 3D QSAR analyses of antimalarial alkoxylated and hydroxylated chalcones were first conducted by Comparative molecular field analysis (CoMFA) and Comparative similarity indices analysis (CoMSIA) to determine the factors required for the activity of these compounds. Satisfactory results were obtained after performing a leave-one-out (LOO) cross-validation study with cross-validation q(2) and conventional r(2) values of 0.740 and 0.972 by the CoMFA model, 0.714 and 0.976 by the CoMSIA model, respectively. The results provided the tools for predicting the affinity of related compounds, and for guiding the design and synthesis of novel and more potent antimalarial agents.

Imidazoline binding sites and their ligands: an overview of the different chemical structures

Since Bousquet et al. discovered the imidazoline binding sites (IBS) two decades ago, when they realized that the antihypertensive drug clonidine interacts not only with the alpha2-adrenenoceptors (alpha2-AR) but also with a distinct imidazoline preferring binding site, these receptors have been paid a great deal of attention. At least two subtypes, I1 and I2, have been characterised based on their binding affinity for different radioligands, but their structures still remain unknown. The pharmacological profile of these IBSs has been the objective of several and very thorough reviews. However, a medicinal chemistry overview of the different IBS ligands prepared to date has never been attempted. In this study, we attempt to compile all the different chemical structures reported to date as IBS ligands and classify them in function of their chemical structure and binding affinity for the different IBS subtypes. Thus, we comment on the different endogenous IBS ligands known as well as the drugs described to interact with the I1-IBS which have found application as antihypertensive drugs. Then, we review those compounds described in the literature to interact with the I2-IBS, classifying them by their chemical families (imidazolines, guanidines, 2-aminoimidazolines, beta-carbolines). Finally, some conclusions are drawn.

Derivation of preliminary three-dimensional pharmacophores for nonhalogenated volatile anesthetics

We investigated the molecular basis for the immobilizing activity of nonhalogenated volatile anesthetics by using comparative molecular field analysis (CoMFA). In vivo potency data (expressed as minimum alveolar anesthetic concentrations) for 38 structurally diverse drugs were obtained from the literature. The anesthetics were randomly divided into a training-set (n = 28) used to formulate the activity models and a test-set (n = 10) used to independently assess the models' predictive power. The anesthetic structures were aligned to maximize their similarity in molecular shape and electrostatic potential to conformers of the most active drug in the group: hexanol. The individual conformers and alignments with maximum similarity (calculated with combined Carbo indices) were retained and used to derive the CoMFA activity models. The final CoMFA model explained 95.5% of the variance in the observed activities of the training-set anesthetics. The model had good predictive capability for both the training-set drugs (cross-validated r(2) = 0.824) and the randomly excluded test-set anesthetics (r(2) = 0.921). Pharmacophoric maps were derived by identifying the spatial distribution of key areas in which steric and electrostatic interactions are important in determining the immobilizing activity of the anesthetics considered.

3D-QSAR illusions

3D-QSAR is typically used to construct models (1) to predict activities, (2) to illustrate significant regions, and (3) to provide insight into possible interactions. To the contrary, examples are described herein which make it clear that the predictivity of such models remains elusive, that so-called significant regions are subject to the vagaries of alignment, and that the nature of possible interactions heavily depends on the eye of the beholder. Although great strides have been made in the imaginative use of 3D-descriptors, 3D-QSAR remains largely a retrospective analytical tool. The arbitrary nature of both the alignment paradigm and atom description lends itself to capricious models, which in turn can lead to distorted conclusions. Despite these illusionary pitfalls, predictions can be enhanced when the test set is bounded by the descriptor space represented in the training set. Interpretation of significant interaction regions becomes more meaningful when alignment is constrained by a binding site. Correlations obtained with a variety of atom descriptors suggest choosing useful ones, in particular, in guiding synthetic effort.

Derivation of preliminary three-dimensional pharmacophoric maps for chemically diverse intravenous general anaesthetics † †This work was supported in part by a project grant from the British Journal of Anaesthesia. It was presented in part at the Anaesthetic Research Society meeting, Cardiff, July 2002 and published in abstract form in the Br J Anaesth 2002; 89: 672–673P

BACKGROUND

The molecular basis of i.v. general anaesthetic activity was investigated using comparative molecular field analysis (CoMFA).

METHODS

The free plasma concentrations that abolish movement to a noxious stimulus for 14 structurally diverse i.v. anaesthetics were obtained from the literature. The compounds were randomly divided into a training set (n=10) to derive the activity model, and a separate test set (n=4) used to assess its predictive capability. The anaesthetic structures were aligned so as to maximize their similarities in molecular shape and electrostatic potential to conformers of the most active agent in the group, eltanolone. The conformers and alignments that showed the maximum similarity (calculated using combined Carbo indices) were retained, and used to derive the CoMFA models.

RESULTS

The final model explained 94.0% of the variance in the observed activities of the training set (n=10, P<0.0001) and was a good predictor of test set activity (n=4, r(2)=0.799). In contrast, a model based on non-polar solubility (LogP) explained only 78.3% of the variance in the observed activities of the training set (n=10, P=0.0007) and was a poor predictor for the test set (n=4, r(2)=0.272). Further analysis of the CoMFA results identified the spatial distribution of key areas where steric and electrostatic interactions are important in determining the activity of the 14 anaesthetics considered.

CONCLUSIONS

A single activity model can be formulated for i.v. general anaesthetics and preliminary pharmacophoric maps derived, which describe the molecular basis of their in vivo potency.

Binding of an imidazopyridoindole at imidazoline I2 receptors

3,5,6,11-Tetrahydro-2H-imidazo[1',2':1,2]pyrido[3,4-b]indole (10) might be viewed as a fusion structure of two classes of I(2) imidazoline receptor ligands: 2-(2-benzofuranyl)-2-imidazolines and beta-carbolines. Its high affinity (K(i)=7.3 nM) provides insight to how the two classes of agents might bind relative to one another at I(2) receptors.

2-(4,5-Dihydro-1H-imidazol-2-yl)indazole (indazim) derivatives as selective I2 imidazoline receptor ligands

A series of variously substituted 2-(4,5-dihydro-1H-imidazol-2-yl)indazoles 3a-j and 2-(4,5-dihydro-1H-imidazol-2-yl)-4,5,6,7-tetrahydroindazole 6 were prepared by the regiospecific heteroalkylation of corresponding indazoles 1a-k with 2-chloro-4,5-dihydroimidazole (2). Their affinity to imidazoline I(2) receptors and alpha(2)-adrenergic receptors was determined by radioligand binding assay carried out on P(2) membrane preparations obtained from rat whole brains. 4-Chloro-2-(4,5-dihydro-1H-imidazol-2-yl)indazole (3f, 4-Cl-indazim) showed a 3076-fold difference in affinity for the [(3)H]2BFI-labeled imidazoline I(2) receptors relative to the [(3)H]RX821001-labeled alpha(2)-adrenergic receptors. This highly selective compound should prove to be useful tool in further understanding the functions of the imidazoline I(2) receptors.

Synthesis and biological evaluation of new 2-(4,5-dihydro-1H-imidazol-2-yl)-3,4-dihydro-2H-1,4-benzoxazine derivatives

2-(4,5-Dihydro-1H-imidazol-2-yl)-3,4-dihydro-2H-1,4-benzoxazine derivatives and tricyclic analogues with a fused additional ring on the nitrogen atom of the benzoxazine moiety have been prepared and evaluated for their cardiovascular effects as potential antihypertensive agents. The imidazoline ring was generated by reaction of the corresponding ethyl ester with ethylenediamine. Affinities for imidazoline binding sites (IBS) I(1) and I(2) and alpha(1) and alpha(2) adrenergic receptors were evaluated as well as the effects on mean arterial blood pressure (MAP) and heart rate (HR) of spontaneously hypertensive rats. With few exceptions the most active compounds on MAP were those with high affinities for IBS and alpha(2) receptor. Among these, compound 4h was the most interesting and is now, together with its enantiomers, under complementary pharmacological evaluation.

Studies of 3D-quantitative structure-activity relationships on a set of nitroaromatic compounds: CoMFA, advanced CoMFA and CoMSIA

By using comparative molecular field analysis (CoMFA), advanced CoMFA and comparative molecular similarity index analysis (CoMSIA) methods, the 3D relationships between the structures of 35 nitroaromatic compounds and their toxicities have been investigated to yield statistically reliable models of considerable predictive power. In contrast to CoMFA, CoMSIA produces better results for the correlation. Moreover, the obtained CoMSIA contour maps that interpret the correlations in terms of field contributions allow physicochemical properties relevant for binding to be easily mapped back onto molecular structures, and thus elucidate structural features among ligands that are responsible for toxicities. Besides, most of the highlighted regions in CoMSIA and CoMFA contour maps are mirrored by features in the surrounding environment. Thereby, CoMFA and CoMSIA both help to give explanations of the toxic mechanism of tested compounds.

I(2)-imidazoline binding site affinity of a structurally different type of ligands

Two families of compounds with affinity towards the I(2) imidazoline binding sites are reported. The first is a family of compounds structurally related to agmatine with two guanidine or 2-aminoimidazoline groups at each end of an aliphatic chain of six, eight, nine or 12 methylene groups. Second, and following the model of clonidine, we propose another family of compounds also with two guanidine or 2-aminoimidazoline groups at each end of a chain consisting of two phenyl rings connected by groups such as CH(2), CO, NH and SO(2). The affinity of the compounds towards the I(2) imidazoline binding sites was then evaluated in human brain tissues. In order to determine their pharmacological selectivity versus alpha(2)-adrenoceptors, the affinity for these receptors was also evaluated for the compounds with the highest affinities at I(2) imidazoline binding sites. The results obtained show that many of the compounds exhibit a considerable affinity towards the I(2) imidazoline binding sites. The aliphatic derivatives, in particular, present a very interesting selectivity for the I(2) imidazoline binding sites versus the alpha(2) adrenoceptors. To better understand these findings, mono-guanidinium analogues of the aliphatic derivatives were synthesised and tested showing poor affinity for I(2) imidazoline binding sites. The importance of these results lies in the novelty of the chemical structures studied (dicationic aliphatic compounds particularly) because they are significantly different to those of the I(2) imidazoline binding site ligands reported to date.

Guanidinium and aminoimidazolinium derivatives of N-(4-piperidyl)propanamides as potential ligands for mu opioid and I2-imidazoline receptors: synthesis and pharmacological screening

Derivatives of N-(1-phenethyl-4-piperidyl)propanamides incorporating guanidinium and 2-aminoimidazolinium groups have been prepared by a synthetic approach involving first introduction of a spacer between the piperidine and the functional group by reductive amination of piperidinone. The formation of each of these functional groups was carried out using N-N'-di(tert-butoxycarbonyl)thiourea and 2-methylthioimidazolinium iodide, respectively. These structures have been designed to incorporate two pharmacologic goals into one entity. Radioligand binding assays have been used to study their affinity for opioid (mu, delta and kappa) and I2-imidazoline receptors. Two of them, 10 and 16, showed high affinity for mu opioid receptors and functionally they had moderate analgesic properties in the hot plate and writhing tests. The in vitro studies on guinea pig ileum (GPI) indicated that both compounds are mu opioid agonists. In what concerns I2-imidazoline receptor activity, these derivatives showed low affinity around 6 to 7 times less than idazoxan.

Can molecular similarity-activity models for intravenous general anaesthetics help explain their mechanism of action?

BACKGROUND

The importance of molecular shape and electrostatic potential in determining the activities of 11 structurally-diverse i.v. general anaesthetics was investigated using computational chemistry techniques.

METHODS

The free plasma anaesthetic concentrations that abolished the response to noxious stimulation were obtained from the literature. The similarities in the molecular shapes and electrostatic potentials of the agents to eltanolone (the most potent anaesthetic agent in the group) were calculated using Carbo indices, and correlated with in vivo potency.

RESULTS

The best model obtained was based on the similarities of the anaesthetics to two eltanolone conformers (r2=0.820). This model correctly predicted the potencies of the R- and S-enantiomers of ketamine, but identified alphaxalone as an outlier. Exclusion of alphaxalone substantially improved the activity correlation (r2=0.972). A bench mark model based on octanol/water partition coefficients (r2=0.647) failed to predict the potency order of the ketamine enantiomers.

CONCLUSIONS

The results demonstrate that a single activity model can be formulated for chiral and non-chiral i.v. anaesthetic agents using molecular similarity indices.

Synthesis of Imidazoles and Imidazolines from 1,2-Diamines and Ethyl (E)- and (Z)-3-Aryl-3-Chloro-2-Cyanopropenoates

Ethyl ( E)- and ( Z)-3-aryl-3-chloro-2-cyanopropenoates react stereoselectively with 1,2-diamines at room temperature to give ethyl ( Z)-3-(2-aminophenylamino)-3-aryl-2-cyanopropenoates, whereas at higher temperatures cyclisation takes place and imidazoles and imidazolines are formed in moderate to high yields.