Rare disease registries classification and characterization: a data mining approach

BACKGROUND

The European Commission and Patients Organizations identify rare disease registries (RDRs) as strategic instruments to develop research and improve knowledge in the field of rare diseases. Interoperability between RDRs is needed for research activities, validation of therapeutic treatments, and public health actions. Sharing and comparing information requires a uniform and standardized way of data collection, so levels of interconnection between RDRs with similar aims and/or nature of data should be identified. The objective of this study is to define a classification and characterization of RDRs in order to identify different profiles and informative needs.

METHODS

Exploratory statistical analyses (cluster analysis and random forest) were applied to data derived from the EPIRARE project ('Building Consensus and Synergies for the EU Rare Disease Patient Registration') survey on the activities and needs of RDRs.

RESULTS

The cluster analysis identified 3 main typologies of RDRs: public health, clinical and genetic research, and treatment registries. The analysis of the most informative variables, identified by the random forest method, led to the characterization of 3 types of RDRs and the definition of different profiles and informative needs.

CONCLUSIONS

These results represent a useful source of information to facilitate the harmonization and interconnection of RDRs in accordance with the different profiles identified. It could help sharing the information between RDRs with similar profiles and, whenever possible, interconnections between registries with different profiles.

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.

Combining structure- and ligand-based approaches for studies of interactions between different conformations of the hERG K+ channel pore and known ligands

Drug-induced insurgence of cardiotoxic effects signaled by the prolongation of the QT interval in the electrocardiogram, has the potential to evolve into a characteristic arrhythmic event named Torsade de Pointes (TdP). Although several different mechanisms can theoretically lead to prolonged QT interval, most of drugs showing this side effect, prolong the cardiac repolarization time through the inhibition of the rapid component of the delayed repolarizing current (IKr) which in humans is carried by a K(+) channel protein encoded by hERG. In this study, four 3D-models, representing different conformational states of hERG K(+) channel, were built by a homology-based technique. A dataset of 59 compounds was collected from the literature and rationally selected according to the availability of IC50 values derived from whole-cell patch clamp performed at 37 °C on HEK cells. Molecular docking was carried out on each one of the four conformations of the channel, hundreds of docking-based molecular descriptors were obtained and used, together with other 2D and 3D molecular descriptors, to develop QSAR models. The statistical parameters describing the accordance between predicted and experimental data and the interpretation of the QSAR models enabled us to assess the reliability of the four 3D-models of the channel pore, thus allowing to look in more depth at binding modes and key features of the interactions occurring between the hERG K(+) channel and ligands endowed of blocking activity.

Planarians as a model to assess in vivo the role of matrix metalloproteinase genes during homeostasis and regeneration

Matrix metalloproteinases (MMPs) are major executors of extracellular matrix remodeling and, consequently, play key roles in the response of cells to their microenvironment. The experimentally accessible stem cell population and the robust regenerative capabilities of planarians offer an ideal model to study how modulation of the proteolytic system in the extracellular environment affects cell behavior in vivo. Genome-wide identification of Schmidtea mediterranea MMPs reveals that planarians possess four mmp-like genes. Two of them (mmp1 and mmp2) are strongly expressed in a subset of secretory cells and encode putative matrilysins. The other genes (mt-mmpA and mt-mmpB) are widely expressed in postmitotic cells and appear structurally related to membrane-type MMPs. These genes are conserved in the planarian Dugesia japonica. Here we explore the role of the planarian mmp genes by RNA interference (RNAi) during tissue homeostasis and regeneration. Our analyses identify essential functions for two of them. Following inhibition of mmp1 planarians display dramatic disruption of tissues architecture and significant decrease in cell death. These results suggest that mmp1 controls tissue turnover, modulating survival of postmitotic cells. Unexpectedly, the ability to regenerate is unaffected by mmp1(RNAi). Silencing of mt-mmpA alters tissue integrity and delays blastema growth, without affecting proliferation of stem cells. Our data support the possibility that the activity of this protease modulates cell migration and regulates anoikis, with a consequent pivotal role in tissue homeostasis and regeneration. Our data provide evidence of the involvement of specific MMPs in tissue homeostasis and regeneration and demonstrate that the behavior of planarian stem cells is critically dependent on the microenvironment surrounding these cells. Studying MMPs function in the planarian model provides evidence on how individual proteases work in vivo in adult tissues. These results have high potential to generate significant information for development of regenerative and anti cancer therapies.

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.

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.

Cytotoxic activity of polyacetylenes and polyenes isolated from roots of Echinacea pallida

BACKGROUND AND PURPOSE

The n-hexane extracts of the roots of three medicinally used Echinacea species exhibited cytotoxic activity on human cancer cell lines, with Echinacea pallida found to be the most cytotoxic. Acetylenes are present in E. pallida lipophilic extracts but essentially absent in extracts from the other two species. In the present study, the cytotoxic effects of five compounds, two polyacetylenes (namely, 8-hydroxy-pentadeca-(9E)-ene-11,13-diyn-2-one (1) and pentadeca-(9E)-ene-11,13-diyne-2,8-dione (3)) and three polyenes (namely, 8-hydroxy-pentadeca-(9E,13Z)-dien-11-yn-2-one (2), pentadeca-(9E,13Z)-dien-11-yne-2,8-dione (4) and pentadeca-(8Z,13Z)-dien-11-yn-2-one (5)), isolated from the n-hexane extract of E. pallida roots by bioassay-guided fractionation, were investigated and the potential bioavailability of these compounds in the extract was studied.

EXPERIMENTAL APPROACH

Cytotoxic effects were assessed on human pancreatic MIA PaCa-2 and colonic COLO320 cancer cell lines. Cell viability was evaluated by the WST-1 assay and apoptotic cell death by the cytosolic internucleosomal DNA enrichment and the caspase 3/7 activity tests. Caco-2 cell monolayers were used to assess the potential bioavailability of the acetylenes.

KEY RESULTS

The five compounds exhibited concentration-dependent cytotoxicity in both cell types, with a greater potency in the colonic cancer cells. Apoptotic cell death was found to be involved in the cytotoxic effect of the most active, compound 5. Compounds 2 and 5 were found to cross the Caco-2 monolayer with apparent permeabilities above 10 x 10(-6) cm s(-1).

CONCLUSIONS AND IMPLICATIONS

Compounds isolated from n-hexane extracts of E. pallida roots have a direct cytotoxicity on cancer cells and good potential for absorption in humans when taken orally.

Structural perturbation of alphaB-crystallin by zinc and temperature related to its chaperone-like activity

alphaB-crystallin is a small heat shock protein that shows chaperone-like activity, as it protects the aggregation of denatured proteins. In this work, the possible relationships between structural characteristics and the biological activity of alphaB-crystallin were investigated on the native protein and on the protein undergoing the separate effects of metal ligation and temperature. The chaperone-like activity of alphaB-crystallin increased in the presence of zinc and when temperature was increased. By using fluorescent probes to monitor hydrophobic surfaces on alphaB-crystallin, it was found that exposed hydrophobic patches on the protein surface increased significantly both in the presence of zinc and when the temperature was raised from 25 to 37 degrees C. The zinc-induced increased exposure of lipophilic residues is in agreement with theoretical calculations performed on 3D-models of monomeric alphaB-crystallin, and may be significant to its increased biological activity.

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.

Understanding the Selectivity Mechanism of the Human Asialoglycoprotein Receptor (ASGP-R) toward Gal- and Man-type Ligands for Predicting Interactions with Exogenous Sugars

A practical approach for addressing the computer simulation of protein-carbohydrate interactions is described here. An articulated computational protocol was set up and validated by checking its ability to predict experimental data, available in the literature, and concerning the selectivity shown by the Carbohydrate Recognition Domain (CRD) of the human asialoglycoprotein receptor (ASGP-R) toward Gal-type ligands. Some required features responsible for the interactions were identified. Subsequently the same protocol was applied to monomer sugar molecules that constitute the building blocks for alginates and ulvans. Such sugar polymers may supply a low-cost source of rare sugars with a potential impact on several industrial applications, from pharmaceutical to fine chemical industry. An example of their applicative exploitation could be given by their use in developing biomaterial with adhesion properties toward hepatocytes, through interaction with the ASGP-R. Such a receptor has been already proposed as a target for exogenous molecules, specifically in the case of hepatocytes, for diagnostic and therapeutic purposes. The DOCK5.2 program was used to search optimal locations of the above ligands of interest into CRD binding site and to roughly estimate interaction energies. Finally, the binding ΔG of theoretical protein-ligand complexes was estimated by using the DelPhi program in which the solvation free energy is accounted for with a continuum solvent model, by solving the Poisson-Boltzmann equation. The structure analysis of the obtained complexes and their ΔG values suggest that one of the sugar monomers of interest shows the desired characteristics.

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.

Binding free energy calculations of adenosine deaminase inhibitors

The interactions between four inhibitors and adenosine deaminase (ADA) were examined by calculating their binding free energies after molecular dynamics simulations. A bonded model was used to represent the electrostatic potentials of the zinc coordination site. The charge distribution of the model was derived by using a two-stage electrostatic potential fitting calculations. The calculated binding free energies are in good agreement with the experimental data and the ranking of binding affinities is well reproduced. Notably, our findings suggest that non-polar contributions play an important role for ADA-inhibitor interactions.

2,9-disubstituted-N6-(arylcarbamoyl)-8-azaadenines as new selective A3 adenosine receptor antagonists: synthesis, biochemical and molecular modelling studies

A number of N6-(N-arylcarbamoyl)-2-substituted-9-benzyl-8-azaadenines, obtained by a modification of the synthetic scheme used to prepare selective A1 ligands, by only three or two steps, are described. At first we prepared a series of 2-phenyl-9-benzyl-8-azaadenines having as N6 substituent a variously substituted N-phenylcarbamoyl group. Some of these derivatives demonstrated good affinity towards the A3 subtype but low selectivity. Compounds having p-CF3, p-F and p-OCH3, as substituents on the phenylcarbamoyl group were selected as lead compounds for the second part of this study. Without modifying the N6 substituent, which would assure A3 affinity, we varied the 9 and 2 positions on these molecules to enhance selectivity. Some compounds having a p-methyl group on the 2-phenyl substituent showed a very good affinity and selectivity for the A3 subtype, revealing the first class of A3 adenosine receptor selective antagonists with a bicyclic structure strictly correlated to the adenine nucleus. The molecular modelling work, carried out using the DOCK program, supplied two models which may be useful for a better understanding of the binding modes. Both models highlighted the preferred interacting tautomeric forms of the antagonists for human A1 and A3 receptors.

QSAR study on thiazole and thiadiazole analogues as antagonists for the adenosine A1 and A3 receptors

Thiazole and thiadiazole analogues have been recently proposed as a novel promising class of adenosine A1 and A3 receptor antagonists. When appropriately modified, they show selectivity toward A1 or A3 receptors, which results in a variety of therapeutic potentialities of these ligands. In this work, we carried out a QSAR study on thiazole and thiadiazole analogues as antagonists for adenosine A1 and A3 receptors. To develop reliable models, we focused attention on any possible pitfalls of each step of QSAR process and approached each stage following accurate procedures. Application of datasets by using CODESSA software led to QSAR equations based on three and four descriptors for the adenosine A1 and A3 receptor ligands, respectively. The obtained models allowed us to understand the main structural features that strongly correlate with the target property.

A modeling study of αB-crystallin in complex with zinc for seeking of correlations between chaperone-like activity and exposure of hydrophobic surfaces

Three-dimensional models for alphaB-crystallin and its complex with zinc were obtained by molecular homology modeling and quantum mechanical calculations in order to explain the effect of the metal on the chaperone-like activity of alphaB-crystallin. In fact, measurements of the chaperone-like activity of alphaB-crystallin revealed that it is significantly increased in presence of the zinc. The theoretical models allowed us to estimate the increased exposition of hydrophobic residues caused by the presence of zinc, suggesting a relationship between structural changes and the increased chaperone-like activity.

A DFT investigation of the addition reaction of monomeric lithium enolate derived from propiophenone to propene oxide: examination of the possible transition structures

The addition reaction of monomeric lithium enolate (Z)-1, derived from propiophenone, to propene oxide 2, was examined to clarify the exact geometry of the transition state (TS) involved in this type of reaction. The eight possible TSs and the corresponding pathways, four leading to syn gamma-hydroxy ketone (gamma-HK) 3 and four leading to anti gamma-HK 4, were compared, using the B3LYP/6-31+G(d)//B3LYP/6-31+G(d) theory level in vacuo and in the presence of the reaction solvent (toluene/hexane). In every case, the favored pathway involves a TS where the enolate C=C and the epoxide C-C are in a gauche relationship and where the Li(+) is stabilized by some C-C and C-H sigma bonds of epoxide 2.

Analysis of the internal representations developed by neural networks for structures applied to quantitative structure--activity relationship studies of benzodiazepines

An application of recursive cascade correlation (CC) neural networks to quantitative structure-activity relationship (QSAR) studies is presented, with emphasis on the study of the internal representations developed by the neural networks. Recursive CC is a neural network model recently proposed for the processing of structured data. It allows the direct handling of chemical compounds as labeled ordered directed graphs, and constitutes a novel approach to QSAR. The adopted representation of molecular structure captures, in a quite general and flexible way, significant topological aspects and chemical functionalities for each specific class of molecules showing a particular chemical reactivity or biological activity. A class of 1,4-benzodiazepin-2-ones is analyzed by the proposed approach. It compares favorably versus the traditional QSAR treatment based on equations. To show the ability of the model in capturing most of the structural features that account for the biological activity, the internal representations developed by the networks are analyzed by principal component analysis. This analysis shows that the networks are able to discover relevant structural features just on the basis of the association between the molecular morphology and the target property (affinity).

A 3D model for the human hepatic asialoglycoprotein receptor (ASGP-R)

The human hepatic Asialoglycoprotein Receptor (ASGP-R) consists of two different types of liver specific membrane glycoproteins that bind to terminal galactose and N-acetylgalactosamine residues of serum glycoproteins. The two different polypeptide chains are referred to as two receptor subunits, HH1 and HH2, which are both involved in the activity of the functional receptor. This receptor has served as a model for understanding receptor-mediated endocytosis and carbohydrate mediated recognition phenomena. Here models for the C-terminal extracellular region of both HH1 and HH2 subunit are presented. The standard homology building procedure was modified in order to make it suitable for the modeling problem at hand. The models for the extracellular regions of HH1 and HH2 were initially constructed by exploiting several fragments, belonging to proteins of known 3D structure, and showing high local sequence similarity with respect to the glycoproteins of interest. Putative binding sites were first hypothesized on the basis of the comparison with other complexes of lectins, the crystal structure of which was available in the Protein Data Bank. A model for the complex involving the HH2 subunit and the typical high affinity ligand N-acetylgalactosamine (NacGal) was refined as the first by a suitable combination of MD simulations and Energy Minimization calculations, since it seemed to quickly converge to a plausible structure. An intermediate model for HH1 was then rebuilt on the basis of the refined model for HH2. It was then submitted to a sequence of molecular dynamics simulations with templates which took into account the secondary structure prediction for a final refinement. The structures of small regions of the models, located around the binding sites, were compared with more recent crystallographic data regarding a complex involving the mutant of Mannose Binding Protein QPDWGH (1BCH entry in the Protein Data Bank) and NacGal. This mutant shows high local sequence similarity with HH1 and HH2 at the binding sites. On the basis of the above comparison, different locations of the binding sites were also considered. In addition to other expected interactions, two hydrophobic interactions were observed in the models with Trp residues (positions 243 in HH1 and 181 or 267 in HH2 respectively) and His residues (positions 256 in HHI and 184 in HH2.respectively). The quality of the models was evaluated by the Procheck program and they seemed plausible. This observation together with analogies found between binding sites of the models and IBCH supported the validity of the models. A further validation element arose by comparison between experimental binding data available in the literature about the homologous rat receptor subunits and theoretical interaction energies evaluated, by means of the DOCK 3.5 program, in models for the rat subunits obtained from the corresponding human ones. The new modeling procedure used here appears to be a well-suited method for structural analysis of small regions, located around the ligands, in proteins of unknown 3D structure.

Nuclear magnetic resonance structure of d(GCATATGATAG). d(CTATCATATGC): a consensus sequence for promoters recognized by sigma K RNA polymerase

The three-dimensional structure of d(GCATATGATAG).d(CTATCATATGC), from the promoter region of a gene regulating sporulation in Bacillus subtilis mother cells, was determined utilizing two-dimensional nuclear Overhauser effect (2D NOE) and double-quantum-filtered COSY (2QF-COSY) spectra. To minimize the effect of methods used to obtain restraints and refine structure, several variables were studied. Interproton distance bounds were calculated very conservatively by running the complete relaxation matrix program MARDIGRAS hundreds of times using 2D NOE spectra for exchangeable and for nonexchangeable protons at different mixing times, assuming different overall correlation times and different starting structures. The 435 distance restraints were used with two different structural refinement methods: restrained molecular dynamics (rMD) and restrained Monte Carlo calculations (rMC). Refinement using different procedures and starting structures resulted in essentially the same structure (<0.8 A rmsd), indicating that the structure is defined by experimental restraints and not the refinement method or variables used. R factors indicate the structures fit the experimental NOE data very well. Some helical parameters, notably large negative X displacement, are characteristic of A-DNA, but others are characteristic of B-DNA. As with TG.CA steps in other duplex DNA sequences studied in our laboratory, the two TG.CA steps have a positive roll, with T6-G7 exhibiting the largest, and consequently a bent helix axis. The converged structure represents a time-averaged structure. However, multiple conformations, especially in deoxyriboses, were evident from vicinal coupling constants obtained from quantitative simulations of 2QF-COSY cross-peaks and from persistent inconsistencies in experimental distances due to nonlinear conformational averaging.

A 3D model of the human A1 adenosine receptor. An evaluation of the binding free-energy with ligands

A model of A1 adenosine receptor was built on the basis of the prediction of transmembrane helices made by PHDtopology and forcing the rough initial model over the scaffold of the rhodopsin. Only helices were accurately modeled. Several complexes between the model of the A1 receptor and some ligands were built. The binding site was hypothesized on the basis of biochemical experiments (site directed mutagenesis). Ligands were selected so that their Kis range between millimolar to nanomolar. The validation of the model was carried out performing calculations of the binding free energy between ligands and the receptor model. The free energy calculations were accomplished by using the linear free energy approximation method (LIE). We could observe that the trend of the calculated delta delta Gs (differences in binding free energies between the antagonist 2, showing the lowest Ki, and the other antagonists analyzed) agreed with the one obtained from biological data.

Synthesis of 2-methylaminobenzimidazole derivatives tested for antiinflammatory activity

A series of 1-alkyl substituted 2-methylaminobenzimidazole derivatives was prepared and tested. Some of them were assayed orally in the rat for antiinflammatory and analgesic properties. The compounds did not exhibit any significant activity compared with reference drug levels.

Benzodiazepine receptor affinity and interaction of some N-(indol-3-ylglyoxylyl)amine derivatives

Several derivatives, in which tryptamine, tyramine, and dopamine moieties are linked to the indole nucleus by an oxalyl bridge, were tested for their ability to displace the specific binding of [3H]flunitrazepam from bovine brain membranes. GABA ratio and in vivo tests for the most potent compounds showed they behave as inverse agonists at the benzodiazepine receptor (BzR). To better define the structure-activity relationship (SAR) of this kind of ligand, several phenylethylamine derivatives were synthesized to evaluate their affinity to BzR. Some of these derivatives (17, 21, 24, 26, and 30) were found to exhibit high affinity (Ki = 0.51-0.085 microM) for BzR and possessed a partial agonist activity, although their chemical structure is closely related to tryptamine 2-6, tyramine 7-11, and dopamine 12-16 derivatives. A different interaction of these ligands to the receptor site is hypothesized. Moreover, all the prepared 1-methyl derivatives exhibited very low binding affinity to BzR.

Solution structure of [d(GGTATACC)]2: wrinkled D structure of the TATA moiety

Phase-sensitive two-dimensional nuclear Overhauser effect spectra of [d(GGTATACC)]2 in aqueous deuterium oxide solution at four mixing times were quantified to give all nonoverlapping cross-peak intensities. A structural model for [d(GGTATACC)]2 was built in which the GG- and -CC moieties were in the B-DNA form, while the middle -TATA- moiety was in the wrinkled-D form (BDB model). This model was subjected to energy refinement by molecular mechanics calculations with the program AMBER. Counterions (Na+) were added to neutralize the charges, and water molecules were placed bridging across the minor groove. A complete relaxation matrix analysis was used to calculate two-dimensional nuclear Overhauser effect spectra of [d(GGTATACC)]2 from the above models (before and after energy refinement) and from four other [d(GGTATACC)]2 structural models: regular A, crystalline A, regular B, and energy-minimized B. Among them, the energy-minimized BDB model yielded a set of theoretical spectra that gave the best fit to the experimental spectra. It was also the energetically most stable. Therefore, it is a good representation of the ensemble- and time-averaged structure of the octamer in solution. This model has backbone torsion angles similar to those of B-form DNA in the GG- and -CC moieties and torsion angles similar to those of wrinkled D form DNA in the -TATA- moiety. The base stacking and base pairing are not interrupted at the junctions between the two structural moieties. Its minor groove is narrower than that of B DNA, and the solvent-accessible surface of the minor groove forms a closed hydration tunnel in the middle -TATA- segment.

A conformational approach to histamine H2-receptor antagonists

Four selective H2-antagonists were studied: burimamide, thiaburimamide, metiamide and cimetidine and their conformations were investigated using the PCILO method. The results show similar preferred conformations but also show that the most active drugs can more easily assume conformations different from the preferred ones. The selective H2-agonist dimaprit was also examined in order to find conformational features determining activity at the H2-histamine receptor.