A Methylene Group on C-2 of 24,24-Difluoro-19-nor-1α,25-dihydroxyvitamin D3 Markedly Increases Bone Calcium Mobilization in Vivo.

Four side chain fluorinated analogues of 1α,25-dihydroxy-19-norvitamin D have been prepared in convergent syntheses using the Wittig-Horner reaction as a key step. Structures and absolute configurations of analogues 3 and 5 were confirmed by X-ray crystallography. All analogues showed high potency in HL-60 cell differentiation and vitamin D-24-hydroxylase (24-OHase) transcription as compared to 1α,25-dihydroxyvitamin D3 (1). Most important is that all of the 20S-configured derivatives (4 and 6) had high bone mobilizing activity in vivo. However, in the 20R series, a 2-methylene group was required for high bone mobilizing activity. A change in positioning of the 20R molecule in the vitamin D receptor when the 2-methylene group is present may provide new insight into the molecular basis of bone calcium mobilization induced by vitamin D.

Selection of a human butyrylcholinesterase-like antibody single-chain variable fragment resistant to AChE inhibitors from a phage library expressed in E. coli.

Organophosphates are potent poisoning agents that cause severe cholinergic toxicity. Current treatment has been reported to be unsatisfactory and novel antidotes are needed. In this study, we used a single-chain variable fragment (scFv) library to select a recombinant antibody fragment (WZ1-14.2.1) with butyrylcholinesterase-like catalytic activity by using an innovative method integrating genetic selection and the bait-and-switch strategy. Ellman assay demonstrated that WZ1-14.2.1 has Michaelis-Menten kinetics in the hydrolysis of all the three substrates used, acetylthiocholine, propionylthiocholine and butyrylthiocholine. Notably, the catalytic activity was resistant to the following acetylcholinesterase inhibitors: neostigmine, iso-OMPA, chlorpyrifos oxon, dichlorvos, and paraoxon ethyl. Otherwise, the enzymatic activity of WZ1-14.2.1 was inhibited by the selective butyrylcholinesterase inhibitor, ethopropazine, and by the Ser-blocking agent phenylmethanesuphonyl fluoride. A hypothetical 3D structure of the WZ1-14.2.1 catalytic site, compatible with functional results, is proposed on the basis of a molecular modeling analysis.

Synthesis and biological activities of vitamin D-like inhibitors of CYP24 hydroxylase.

Selective inhibitors of CYP24A1 represent an important synthetic target in a search for novel vitamin D compounds of therapeutic value. In the present work, we show the synthesis and biological properties of two novel side chain modified 2-methylene-19-nor-1,25(OH)(2)D(3) analogs, the 22-imidazole-1-yl derivative 2 (VIMI) and the 25-N-cyclopropylamine compound 3 (CPA1), which were efficiently prepared in convergent syntheses utilizing the Lythgoe type Horner-Wittig olefination reaction. When tested in a cell-free assay, both compounds were found to be potent competitive inhibitors of CYP24A1, with the cyclopropylamine analog 3 exhibiting an 80-1 selective inhibition of CYP24A1 over CYP27B1. Addition of 3 to a mouse osteoblast culture sustained the level of 1,25(OH)(2)D(3), further demonstrating its effectiveness in CYP24A1 inhibition. Importantly, the in vitro effects on human promyeloid leukemia (HL-60) cell differentiation by 3 were nearly identical to those of 1,25(OH)(2)D(3) and in vivo the compound showed low calcemic activity. Finally, the results of preliminary theoretical studies provide useful insights to rationalize the ability of analog 3 to selectively inhibit the cytochrome P450 isoform CYP24A1.

Identification of selective ligands for human fibrin recognition using high-throughput docking.

The ultimate aim of this study is to identify new molecules that are able to recognize polymerized fibrin, which is the main component of a thrombus. These selective ligands can be exposed on the surface of particular nanoparticles used for the targeted delivery of fibrinolytic drugs. The targeted delivery of these drugs is expected to help to keep under control the severe side effects which can occur if the drugs are administered systemically. The study focuses on the application of high-throughput docking methods used to screen a library of thousands of commercial compounds. The aim was to identify molecules that are potentially capable of interacting with the human fibrin γ(312-324) epitope. The best scoring compounds were purchased and tested through fluorimetric assays in order to estimate their affinity toward fibrin. The results show that the protocol proposed here for identifying new compounds of interest may provide a valuable contribution to the discovery of lead molecules for human fibrin recognition.

Optimizing QSAR models for predicting ligand binding to the drug-metabolizing cytochrome P450 isoenzyme CYP2D6.

The cytochrome P450 isozyme CYP2D6 binds a large variety of drugs, oxidizing many of them, and plays a crucial role in establishing in vivo drug levels, especially in multidrug regimens. The current study aimed to develop reliable predictive models for estimating the CYP2D6 inhibition properties of drug candidates. Quantitative structure-activity relationship (QSAR) studies utilizing 51 known CYP2D6 inhibitors were carried out. Performance achieved using models based on two-dimensional (2D) molecular descriptors was compared with performance using models entailing additional molecular descriptors that depend upon the three-dimensional (3D) structure of ligands. To properly compute the descriptors, all the 3D inhibitor structures were optimized such that induced-fit binding of the ligand to the active site was accommodated. CODESSA software was used to obtain equations for correlating the structural features of the ligands to their pharmacological effects on CYP2D6 (inhibition). The predictive power of all the QSAR models obtained was estimated by applying rigorous statistical criteria. To assess the robustness and predictability of the models, predictions were carried out on an additional set of known molecules (prediction set). The results showed that only models incorporating 3D descriptors in addition to 2D molecular descriptors possessed the requisite high predictive power for CYP2D6 inhibition.

Three-dimensional models of the oligomeric human asialoglycoprotein receptor (ASGP-R).

The work presented here is aimed at suggesting plausible hypotheses for functional oligomeric forms of the human asialoglycoprotein receptor (ASGP-R), by applying a combination of different computational techniques. The functional ASGP-R is a hetero-oligomer, that comprises of several subunits of two different kinds (H1 and H2), which are highly homologous. Its stoichiometry is still unknown. An articulated step-wise modeling protocol was used in order to build the receptor model in a minimal oligomeric form, necessary for it to bind multi-antennary carbohydrate ligands. The ultimate target of the study is to contribute to increasing the knowledge of interactions between the human ASGP-R and carbohydrate ligands, at the molecular level, pertinent to applications in the field of hepatic tissue engineering.

Quantitative structure-activity relationship models for predicting biological properties, developed by combining structure- and ligand-based approaches: an application to the human ether-a-go-go-related gene potassium channel inhibition.

A strategy for developing accurate quantitative structure-activity relationship models enabling predictions of biological properties, when suitable knowledge concerning both ligands and biological target is available, was tested on a data set where molecules are characterized by high structural diversity. Such a strategy was applied to human ether-a-go-go-related gene K(+) channel inhibition and consists of a combination of ligand- and structure-based approaches, which can be carried out whenever the three-dimensional structure of the target macromolecule is known or may be modeled with good accuracy. Molecular conformations of ligands were obtained by means of molecular docking, performed in a previously built theoretical model of the channel pore, so that descriptors depending upon the three-dimensional molecular structure were properly computed. A modification of the directed sphere-exclusion algorithm was developed and exploited to properly splitting the whole dataset into Training/Test set pairs. Molecular descriptors, computed by means of the codessa program, were used for the search of reliable quantitative structure-activity relationship models that were subsequently identified through a rigorous validation analysis. Finally, pIC(50) values of a prediction set, external to the initial dataset, were predicted and the results confirmed the high predictive power of the model within a quite wide chemical space.

Development of QSAR models for predicting hepatocarcinogenic toxicity of chemicals.

A dataset comprising 55 chemicals with hepatocarcinogenic potency indices was collected from the Carcinogenic Potency Database with the aim of developing QSAR models enabling prediction of the above unwanted property for New Chemical Entities. The dataset was rationally split into training and test sets by means of a sphere-exclusion type algorithm. Among the many algorithms explored to search regression models, only a Support Vector Machine (SVM) method led to a QSAR model, which was proved to pass rigorous validation criteria, in accordance with the OECD guidelines. The proposed model is capable to explain the hepatocarcinogenic toxicity and could be exploited for predicting this property for chemicals at the early stage of their development, so optimizing resources and reducing animal testing.

Synthesis, biological assays and QSAR studies of N-(9-benzyl-2-phenyl-8-azapurin-6-yl)-amides as ligands for A1 adenosine receptors.

2-Phenyl-9-benzyl-8-azapurines, bearing at the 6 position an amido group interposed between the 8-azapurine moiety and an alkyl or a substituted phenyl group, have been synthesised and assayed as ligands for adenosine receptors. All the compounds show high affinity for the A(1) adenosine receptor, and many of them also show a good selectivity for A(1) with respect to A(2A) and A(3) adenosine receptors. Based on the quite rich library containing such compounds and relevant biological data, QSAR models, able to rationalise the results and to give a quantitative estimate of the observed trends were also developed. The obtained models can assist in the design of new compounds selectively active on A(1) adenosine receptor.

QSAR studies on BK channel activators.

QSAR studies were developed on the basis of a dataset comprising BK channel activators previously synthesized and biologically assayed in our laboratory, in order to obtain highly accurate models enabling prediction of affinity toward the channel for New Chemical Entities (NCEs). Many molecular descriptors were computed by the CODESSA software. They were initially exploited in order to rationally split the available dataset into training and test set pairs, which supplied the basis for the development of QSAR models. Models were subjected to rigorous validation analysis based on the estimate of several statistical parameters, for the seek of the most accurate and simplest model enabling prediction of BK channel affinity.

Computational modeling and surface plasmon resonance analyses in the assessment of peptide ligands interacting with fibrin gamma(312-324) epitope.

Fibrin represents a suitable target for addressing delivery systems loaded by fibrinolytic drugs. Selective ligands capable to recognize fibrin could be used as targeting moieties for such systems. In this study the interactions between the gamma(312-324) epitope of human fibrin and peptidic ligands were analyzed by using experimental and computational methods. Binding free energies were calculated through the molecular mechanics/generalized born surface area approach. Good qualitative agreements between the experimental and calculated data were obtained. The binding affinity seems to be well correlated (R(2)=0.69) with the changes of the nonpolar solvation energy term computed from solvent-accessible surface area calculation. These results indicate that current methods of estimating binding free energies are efficient for achieving information on protein-ligand interactions.

Identification of "toxicophoric" features for predicting drug-induced QT interval prolongation.

Drugs delaying cardiac repolarization by blockade of hERG K(+) channel generally prolong the QT interval of the electrocardiogram, an effect regarded as a cardiac risk factor with the potential to cause 'torsade des pointes'-type arrhythmias in humans. The present study applied a homology building technique and molecular dynamics simulations to model the pore of hERG K(+) channel. A docking analysis was then performed on selected ligands which were classified as QT-prolonging or non-prolonging after experimental measurements in in vivo anesthetized guinea pig. The results of this structural analysis provided a "toxicophoric" model that was further exploited to inspect a dataset of known QT-prolonging/non-prolonging molecules. The emerging major chemical features to be avoided, in order to obtain cardiac safe therapeutic agents, comprise the simultaneous presence of (i) a protonated nitrogen atom within an observed range of distances from a heteroatom; (ii) aromatic groups capable of interacting within an area defined by Gly657 residues of the pore or within an area located at the top of the longitudinal axis of the pore. Moreover, additional hydrophobic moieties interacting with one of the equatorial cavities located in the area near-by Tyr652 residues and/or with a hydrophobic ring defined by Phe656 residues should be avoided.

QSAR study on a novel series of 8-azaadenine analogues proposed as A1 adenosine receptor antagonists.

8-Azaadenines have been recently proposed as a novel promising class of adenosine A1 receptor antagonists. A QSAR study on 45 derivatives, synthesized in our laboratory as antagonists for A1 receptor, is described here. The use of the CODESSA program allowed obtaining a quite simple equation capable of correlating the structural features of these ligands to their activity toward A1 receptor. The model was investigated for reliability and stability by using statistical analysis criteria stricter than usual. Particular care was put in defining the chemical space where the model gave reliable predictions. The model allowed the identification of relevant structural features required for the interaction with the A1 receptor, enabling the prediction of activity of molecules belonging to focused virtual libraries.

Synthesis, biological activity and molecular modelling of new trisubstituted 8-azaadenines with high affinity for A1 adenosine receptors.

We describe here the synthesis and biological activity of new 8-azaadenines bearing both a phenyl group on C(2) and a 9-benzyl group substituted in the ortho position with a Cl or a F atom or a CF(3) group, to verify the synergistic effect of a combination of these substitution patterns on binding with the A(1) adenosine receptors. In position N(6) aliphatic and cycloaliphatic substituents were chosen which had been shown to bind well with the A(1) receptors. Because of the high lipophilicity of these kinds of molecules, we also introduced a hydroxyalkyl substituent in the same position. The compounds obtained generally showed a very good affinity and selectivity for A(1) receptors. Some of the compounds showed K(i) in the nanomolar range, one even in the subnanomolar range (0.6 M). Molecular docking calculations were performed in order to evaluate the interaction energies between the bovine A(1) receptor model and the selected ligands, and then to correlate these energies with biological activities of the ligands as obtained from the experiments. Molecular docking analysis suggests different binding modes towards A(1) receptors that are plausible for these ligands.

Modulation of P-glycoprotein activity by cannabinoid molecules in HK-2 renal cells.

1. Endogenous and synthetic cannabinoid molecules have been investigated as possible MDR-1/P-glycoprotein (P-gp) modulators in HK-2-immortalized renal cells, using calcein acetoxymethylester (calcein-AM) as a P-gp substrate. 2. Among the endocannabinoid molecules tested, anandamide (AEA), but not 2-arachidonoyl-glycerol (2-AG) or palmitoyl-ethanolamide (PEA), increased the intracellular fluorescence emitted by calcein, a metabolic derivative of the P-gp substrate calcein-AM, indicative of a reduction in transport capacity. 3. All the three synthetic cannabimimetics tested, that is, R-(+)-methanandamide (R(+)-MET), AM 251 and CP55,940 significantly increased calcein accumulation in the cytosol. 4. RT-PCR demonstrated that HK-2 cells do not express CB1 or CB2 cannabinoid receptors. 5. R(+)-MET, AM251 and CP55,940 were also evaluated as modulators of P-gp expression, by Western blot analysis. Only AM251 weakly enhanced the protein levels (by 1.2-fold) after a 4-day-long incubation with the noncytotoxic drug concentration 2 microM. 6. The present data provide the first evidence that the endocannabinoid AEA and different synthetic cannabinoids may inhibit the P-gp activity in vitro via a cannabinoid receptor-independent mechanism.

Prediction of hERG potassium channel affinity by the CODESSA approach.

The problem of predicting torsadogenic cardiotoxicity of drugs is afforded in this work. QSAR studies on a series of molecules, acting as hERG K+ channel blockers, were carried out for this purpose by using the CODESSA program. Molecules belonging to the analyzed dataset are characterized by different therapeutic targets and by high molecular diversity. The predictive power of the obtained models was estimated by means of rigorous validation criteria implying the use of highly diagnostic statistical parameters on the test set, other than the training set. Validation results obtained for a blind set, disjoined from the whole dataset initially considered, confirmed the predictive potency of the models proposed here, so suggesting that they are worth to be considered as a valuable tool for practical applications in predicting the blockade of hERG K+ channels.

Design of highly specific ligands of fibrin for therapeutic applications.

The work presented here is aimed at designing high-affinity ligands for the fibrin gamma (312-324) epitope. This epitope is specific for fibrin recognition, as it is exposed only on the fibrin surface, while in fibrinogen it is buried in the protein bulk. This property makes it very useful for therapeutic applications. In fact, it may be exploited in driving systems for targeted delivery of thrombolytic drugs toward the specific compartment where they are needed. It will then allow avoidance of serious unwanted side effects produced by a conventional systemic administration. The approach chosen for designing putative ligands is based on the known three-dimensional (3D) structure of the epitope. A wide virtual library made up of oligo-peptides and analogues designed by a combinatorial approach, on the basis of chemical complementarity criteria, has been screened by means of a docking/scoring approach (DOCK program). The peculiarity of the problem under study required a considerable effort in finding a method enabling the experimental validation of the design work results. In fact the selected biological target is absolutely new, so that neither a endogenous, nor a synthetic high-affinity ligand is known up to now. It does not allow for the validation of computational results by means of classical binding tests based on the use of known labeled high-affinity ligands. Preliminary binding essayes were so carried out by means of the Plasmon Surface Resonance (PSR) technique. The experimental results suggested that most of the molecules predicted to be good ligands by means of the selected computational tools, could carry the wanted affinity toward the selected target.