Chapter 1 : nucleobases with designed patterns of hydrogen bonding

The chemistry used in key bond-forming steps to prepare nucleobases with designed patterns of hydrogen bonding is surveyed. Incorporation of the nucleobases into DNA and RNA oligomers is achieved either chemically using building blocks such as nucleoside phosphoramidites or enzymatically using nucleotide triphosphates. By varying the hydrogen bonding pattern within nucleobases, and by incorporating additional substituents, new structures have been designed that "reach over" so that contacts with both strands in targeted duplex DNA can be made in antigene strategies to control gene expression. Various new base-pairing systems have been evaluated that expand the genetic alphabet beyond Watson-Crick base pairs A.T and G.C. For example, benzo-homologated analogs of the natural DNA bases represent a new genetic set of orthogonal, size-expanded derivatives that have been shown to encode amino acids of a protein in a living organism.

Studies on the hydrogen bonding of organic chemicals

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June Sutor and the C-H…O hydrogen bonding controversy

In 1962, D. June Sutor published the first crystallographic analysis of C–H…O hydrogen bonding based on a selection of structures then known. Her follow-up paper the next year cited more structures and provided more details, but her ideas met with formidable opposition. This review begins by describing knowledge of C-H…O hydrogen bonding available at the time from physico-chemical and spectroscopic studies. By comparison of structures cited by Sutor with modern redeterminations, the soundness of her basic data set is assessed. The plausibility of the counter-arguments against her is evaluated. Finally, her biographical details are presented along with consideration of factors that might have impeded the acceptance of her work. © 2012 Taylor & Francis.

Histidine hydrogen bonding in MHC at pH 5 and pH 7 modeled by molecular docking and molecular dynamics simulations

Hydrogen bonds play important roles in maintaining the structure of proteins and in the formation of most biomolecular protein-ligand complexes. All amino acids can act as hydrogen bond donors and acceptors. Among amino acids, Histidine is unique, as it can exist in neutral or positively charged forms within the physiological pH range of 5.0 to 7.0. Histidine can thus interact with other aromatic residues as well as forming hydrogen bonds with polar and charged residues. The ability of His to exchange a proton lies at the heart of many important functional biomolecular interactions, including immunological ones. By using molecular docking and molecular dynamics simulation, we examine the influence of His protonation/deprotonation on peptide binding affinity to MHC class II proteins from locus HLA-DP. Peptide-MHC interaction underlies the adaptive cellular immune response, upon which the next generation of commercially-important vaccines will depend. Consistent with experiment, we find that peptides containing protonated His residues bind better to HLA-DP proteins than those with unprotonated His. Enhanced binding at pH 5.0 is due, in part, to additional hydrogen bonds formed between peptide His+ and DP proteins. In acidic endosomes, protein His79β is predominantly protonated. As a result, the peptide binding cleft narrows in the vicinity of His79β, which stabilizes the peptide - HLA-DP protein complex. © 2014 Bentham Science Publishers.

The chemical structure and mechanical properties of phenolic resins and related polymers

Paper-based phenolic laminates are used extensively in the electrical industry. Many small components are fabricated from these materials by the process known as punching. Recently an investigation was carried out to study the effect of processing variables on the punching properties. It was concluded that further work would be justified and that this should include a critical examination of the resin properties in a more controlled and systematic manner. In this investigation an attempt has been made to assess certain features of the resin structure in terms of thermomechanical properties. The number of crosslinks in the system was controlled using resins based on phenol and para-cresol formulations. Intramolecular hydrogen bonding effects were examined using substituted resins and a synthetically derived phenol based on 1,3-di-(o-hydroxyphenyl) propane.. A resin system was developed using the Friedel Crafts reaction to examine inter-molecular hydrogen bonding at the resin-paper interface. The punching properties of certain selected resins were assessed on a qualitative basis. In addition flexural and dynamic mechanical properties were determined in a general study of the structure-property relationships of these materials. It has been shown that certain features of the resin structure significantly influenced mechanical properties. :F'urther, it was noted that there is a close relationship between punching properties, mechanical damping and flexural strain. This work includes a critical examination of the curing mechanism and views are postulated in an attempt to extend knowledge in this area of the work. Finally, it is argued that future work should be based on a synthetic approach and that dynamic mechanical testing would provide a powerful tool In developing a deeper understanding of the resin fine structure.

Improving the solubility and dissolution of poorly soluble drugs by salt formation and the consequent effect on mechanical properties

The bioavailability of BCS II compounds may be improved by an enhanced solubility and dissolution rate. Four carboxylic acid drugs were selected, which were flurbiprofen, etodolac, ibuprofen and gemfibrozil. The drugs were chosen because they are weak acids with poor aqueous solubility and should readily form salts. The counterions used for salt formation were: butylamine, pentylamine, hexylamine, octylamine, benzylamine, cyclohexylamine, tert-butylamine, 2-amino-2-methylpropan­2-ol, 2-amino-2-methyl propan-1,3-ol and tromethamine. Solubility was partially controlled by the saturated solution pH with the butylamine counterion increasing the solution pH and solubility and dissolution to the greatest extent. As the chain length increased, solubility was reduced due to the increasing lipophilic nature of the counterion. The benzylamine and cyclohexylamine counterions produced crystalline, stable salts but did not improve solubility and dissolution significantly compared to the parent compound. The substitution of hydroxyl groups to tert-butylamine counterions produced an increase in solubility and dissolution. AMP2 resulted in the most enhanced solubility and dissolution compared to the parent drug but using the tris salt did not further improve solubility due to a very stable crystal lattice structure. The parent drugs were very difficult to compress due to orientation effects and lamination. Compacts were prepared of each parent drug and salt and their modulus of elasticity values were measured using a three-point bend (Young’s modulus, E0) were extrapolated to zero porosity and compared. Compressibility and E0 were improved with the butylamine, tert-butylamine, cyclohexylamine and AMP2 counterions. The most significant improvement in compression and E0 was with the AMP2 salts. Mechanical properties were related to the hydrogen bonding within the crystal lattice structure for the gemfibrozil salt series.

Biological interactions with synthetic polymers

Anchorage dependent cell culture is a useful model for investigating the interface that becomes established when a synthetic polymer is placed in contact with a biological system. The primary aim of this interdisciplinary study was to systematically investigate a number of properties that were already considered to have an influence on cell behaviour and thereby establish the extent of their importance. It is envisaged that investigations such as these will not only further the understanding of the mechanisms that affect cell adhesion but may ultimately lead to the development of improved biomaterials. In this study, surface analysis of materials was carried out in parallel with culture studies using fibroblast cells. Polarity, in it's ability to undergo hydrogen bonding (eg with water and proteins), had an important affect on cell behaviour, although structural arrangement and crystallinity were not found to exert any marked influence. In addition, the extent of oxidation that had occurred during the process of manufacture of substrates was also important. The treatment of polystyrene with a selected series of acids and gas plasmas confirmed the importance of polarity, structural groups and surface charge and it was shown that this polymer was not unique among `hydrophobic' materials in it's inability to support cell adhesion. The individual water structuring groups within hydrogel polymers were also observed to have controlling effects on cell behaviour. An overall view of the biological response to both hydrogel and non-hydrogel materials highlighted the importance of surface oxidation, polarity, water structuring groups and surface charge. Initial steps were also taken to analyse foetal calf serum, which is widely used to supplement cell culture media. Using an array of analytical techniques, further experiments were carried out to observe any possible differences in the amounts of lipids and calcium that become deposited to tissue culture and bacteriological grade plastic under cell culture conditions.

Observed and predicted hydrogen bond motifs in crystal structures of hydantoins, dihydrouracils and uracils

A survey of crystal structures containing hydantoin, dihydrouracil and uracil derivatives in the Cambridge Structural Database revealed four main types of hydrogen bond motifs when derivatives with extra substituents able to interfere with the main motif are excluded. All these molecules contain two hydrogen bond donors and two hydrogen bond acceptors in the sequence of NH, C = O, NH, and C=O groups within a 5-membered ring (hydantoin) and two 6-membered rings (dihydrouracil and uracil). In all cases, both ring NH groups act as donors in the main hydrogen bond motif but there is an excess of hydrogen bond acceptors (two C=O able to accept twice each) and so two possibilities are found: (i) each carbonyl O atom may accept one hydrogen bond or (ii) one carbonyl O atom may accept two hydrogen bonds while the other does not participate in the hydrogen bonding. We observed different preferences in the type and symmetry of the motifs adopted by the different derivatives, and a good agreement is found between motifs observed experimentally and those predicted using computational methods. We identified certain molecular factors such as chirality, substituent size and the possibility of C-H⋯O interactions as important factors influencing the motif observation. © 2012 The Royal Society of Chemistry and the Centre National de la Recherche Scientifique.

Methyl chloride purification for the silicone industry

This study experimentally investigated methyl chloride (MeCl) purification method using an inhouse designed and built volumetric adsorption/desorption rig. MeCl is an essential raw material in the manufacture of silicone however all technical grades of MeCl contain concentrations (0.2 - 1.0 % wt) of dimethyl ether (DME) which poison the process. The project industrial partner had previously exhausted numerous separation methods, which all have been deemed not suitable for various reasons. Therefore, adsorption/desorption separation was proposed in this study as a potential solution with less economic and environmental impact. Pure component adsorption/desorption was carried out for DME and MeCl on six different adsorbents namely: zeolite molecular sieves (types 4 Å and 5 Å); silica gels (35-70 mesh, amorphous precipitated, and 35-60 mesh) and granular activated carbon (type 8-12 mesh). Subsequent binary gas mixture adsorption in batch and continuous mode was carried out on both zeolites and all three silica gels following thermal pre-treatment in vacuum. The adsorbents were tested as received and after being subjected to different thermal and vacuum pre-treatment conditions. The various adsorption studies were carried out at low pressure and temperature ranges of 0.5 - 3.5 atm and 20 - 100 °C. All adsorbents were characterised using Brunauer Emmett Teller (BET), thermogravimetric analysis (TGA), scanning electron microscopy (SEM) and energy dispersive x-ray analysis (EDXA) to investigate their physical and chemical properties. The well-known helium (He) expansion method was used to determine the empty manifold and adsorption cell (AC) regions and respective void volumes for the different adsorbents. The amounts adsorbed were determined using Ideal gas laws via the differential pressure method. The heat of adsorption for the various adsorbate-adsorbent (A-S) interactions was calculated using a new calorimetric method based on direct temperature measurements inside the AC. Further adsorption analysis included use of various empirical and kinetic models to determine and understand the behaviour of the respective interactions. The gas purification behaviour was investigated using gas chromatography and mass spectroscopy (GC-MC) analysis. Binary gas mixture samples were syringed from the manifold iii and AC outlet before and after adsorption/desorption analysis through manual sample injections into the GC-MS to detect and quantify the presence of DME and ultimately observe for methyl chloride purification. Convincing gas purification behaviour was confirmed using two different GC columns, thus giving more confidence on the measurement reliability. From the single pure component adsorption of DME and MeCl on the as received zeolite 4A subjected to 1 h vacuum pre-treatment, both gases exhibited pseudo second order adsorption kinetics with DME exhibiting a rate constant nearly double that of MeCl thus suggesting a faster rate of adsorption. From the adsorption isotherm classification both DME and MeCl exhibited Type II and I adsorption isotherm classifications, respectively. The strength of bonding was confirmed by the differential heat of adsorption measurement, which was found to be 23.30 and 10.21 kJ mol-1 for DME and MeCl, respectively. The former is believed to adsorb heterogeneously through hydrogen bonding whilst MeCl adsorbs homogenously via van der Waal’s (VDW) forces. Single pure component adsorption on as received zeolite 5A, silica gels (35-70, amorphous precipitated and 35-60) resulted in similar adsorption/desorption behaviour in similar quantities (mol kg-1). The adsorption isotherms for DME and MeCl on zeolite 5A, silica gels (35-70, amorphous precipitated and 35-60) and activated carbon 8-12 exhibited Type I classifications, respectively. Experiments on zeolite 5A indicated that DME adsorbed stronger, faster and with a slightly stronger strength of interaction than MeCl but in lesser quantities. On the silica gels adsorbents, DME exhibited a slightly greater adsorption capacity whilst adsorbing at a similar rate and strength of interaction compared to MeCl. On the activated carbon adsorbent, MeCl exhibited the greater adsorption capacity at a faster rate but with similar heats of adsorption. The effect of prolonged vacuum (15 h), thermal pre-treatment (150 °C) and extended equilibrium time (15 min) were investigated for the adsorption behaviour of DME and MeCl on both zeolites 4A and 5A, respectively. Compared to adsorption on as received adsorbents subjected to 1 h vacuum the adsorption capacities for DME and MeCl were found to increase by 1.95 % and 20.37 % on zeolite 4A and by 4.52 % and 6.69 % on zeolite 5A, respectively. In addition the empirical and kinetic models and differential heats of adsorption resulted in more definitive fitting curves and trends due to the true equilibrium position of the adsorbate with the adsorbent. Batch binary mixture adsorption on thermally and vacuum pre-treated zeolite 4A demonstrated purification behaviour of all adsorbents used for MeCl streams containing DME impurities, with a concentration as low as 0.66 vol. %. The GC-MS analysis showed no DME detection for the tested concentration mixtures at the AC outlet after 15 or 30 min, whereas MeCl was detectable in measurable amounts. Similar behaviour was also observed when carrying out adsorption in continuous mode. On the other hand, similar studies on the other adsorbents did not show such favourable MeCl purification behaviour. Overall this study investigated a wide range of adsorbents (zeolites, silica gels and activated carbon) and demonstrated for the first time potential to purify MeCl streams containing DME impurities using adsorption/desorption separation under different adsorbent pre-treatment and adsorption operating conditions. The study also revealed for the first time the adsorption isotherms, empirical and kinetic models and heats of adsorption for the respective adsorbentsurface (A-S) interactions. In conclusion, this study has shown strong evidence to propose zeolite 4A for adsorptive purification of MeCl. It is believed that with a technical grade MeCl stream competitive yet simultaneous co-adsorption of DME and MeCl occurs with evidence of molecular sieiving effects whereby the larger DME molecules are unable to penetrate through the adsorbent bed whereas the smaller MeCl molecules diffuse through resulting in a purified MeCl stream at the AC outlet. Ultimately, further studies are recommended for increased adsorption capacities by considering wider operating conditions, e.g. different adsorbent thermal and vacuum pre-treatment and adsorbing at temperatures closer to the boiling point of the gases and different conditions of pressure and temperature.

αα'-trehalose 6,6'-dibehenate in non-phospholipid-based liposomes enables direct interaction with trehalose, offering stability during freeze-drying

Trehalose is a well known protector of biostructures like liposomes and proteins during freeze-drying, but still today there is a big debate regarding its mechanism of action. In previous experiments we have shown that trehalose is able to protect a non-phospholipid-based liposomal adjuvant (designated CAF01) composed of the cationic dimethyldioctadecylammonium (DDA) and trehalose 6,6-dibehenate (TDB) during freeze-drying [D. Christensen, C. Foged, I. Rosenkrands, H.M. Nielsen, P. Andersen, E.M. Agger, Trehalose preserves DDA/TDB liposomes and their adjuvant effect during freeze-drying, Biochim. Biophys. Acta, Biomembr. 1768 (2007) 2120-2129]. Furthermore it was seen that TDB is required for the stabilizing effect of trehalose. Herein, we show using the Langmuir-Blodgett technique that a high concentration of TDB present at the water-lipid interface results in a surface pressure around 67 mN/m as compared to that of pure DDA which is approximately 47 mN/m in the compressed state. This indicates that the attractive forces between the trehalose head group of TDB and water are greater than those between the quaternary ammonium head group of DDA and water. Furthermore, addition of trehalose to a DDA monolayer containing small amounts of TDB also increases the surface pressure, which is not observed in the absence of TDB. This suggests that even small amounts of trehalose groups on TDB present at the water-lipid interface associate free trehalose to the liposome surface, presumably by hydrogen bonding between the trehalose head groups of TDB and the free trehalose molecules. Hence, for CAF01 the TDB component not only stabilizes the cationic liposomes and enhances the immune response but also facilitates the cryo-/lyoprotection by trehalose through direct interaction with the head group of TDB. Furthermore the results indicate that direct interaction with liposome surfaces is necessary for trehalose to enable protection during freeze-drying.

Models of gas-liquid solubilities

A recent method for phase equilibria, the AGAPE method, has been used to predict activity coefficients and excess Gibbs energy for binary mixtures with good accuracy. The theory, based on a generalised London potential (GLP), accounts for intermolecular attractive forces. Unlike existing prediction methods, for example UNIFAC, the AGAPE method uses only information derived from accessible experimental data and molecular information for pure components. Presently, the AGAPE method has some limitations, namely that the mixtures must consist of small, non-polar compounds with no hydrogen bonding, at low moderate pressures and at conditions below the critical conditions of the components. Distinction between vapour-liquid equilibria and gas-liquid solubility is rather arbitrary and it seems reasonable to extend these ideas to solubility. The AGAPE model uses a molecular lattice-based mixing rule. By judicious use of computer programs a methodology was created to examine a body of experimental gas-liquid solubility data for gases such as carbon dioxide, propane, n-butane or sulphur hexafluoride which all have critical temperatures a little above 298 K dissolved in benzene, cyclo-hexane and methanol. Within this methodology the value of the GLP as an ab initio combining rule for such solutes in very dilute solutions in a variety of liquids has been tested. Using the GLP as a mixing rule involves the computation of rotationally averaged interactions between the constituent atoms, and new calculations have had to be made to discover the magnitude of the unlike pair interactions. These numbers have been seen as significant in their own right in the context of the behaviour of infinitely-dilute solutions. A method for extending this treatment to "permanent" gases has also been developed. The findings from the GLP method and from the more general AGAPE approach have been examined in the context of other models for gas-liquid solubility, both "classical" and contemporary, in particular those derived from equations-of-state methods and from reference solvent methods.

Design and synthesis of potential antimicrobial agents

Tuberculosis is one of the most devastating diseases in the world primarily due to several decades of neglect and an emergence of multidrug-resitance strains (MDR) of M. tuberculosis together with the increased incidence of disseminated infections produced by other mycobacterium in AIDS patients. This has prompted the search for new antimycobacterial drugs. A series of pyridine-2-, pyridine-3-, pyridine-4-, pyrazine and quinoline-2-carboxamidrazone derivatives and new classes of carboxamidrazone were prepared in an automated fashion and by traditional synthesis. Over nine hundred synthesized compounds were screened for their anti mycobacterial activity against M. fortutium (NGTG 10394) as a surrogate for M. tuberculosis. The new classes of amidrazones were also screened against tuberculosis H37 Rv and antimicrobial activities against various bacteria. Fifteen tested compounds were found to provide 90-100% inhibition of mycobacterium growth of M. tuberculosis H37 Rv in the primary screen at 6.25 μg mL-1. The most active compound in the carboxamidrazone amide series had an MIG value of 0.1-2 μg mL-1 against M. fortutium. The enzyme dihydrofolate reductase (DHFR) has been a drug-design target for decades. Blocking of the enzymatic activity of DHFR is a key element in the treatment of many diseases, including cancer, bacterial and protozoal infection. The x-ray structure of DHFR from M. tuberculosis and human DHFR were found to have differences in substrate binding site. The presence of glycerol molecule in the Xray structure from M. tuberculosis DHFR provided opportunity to design new antifolates. The new antifolates described herein were designed to retain the pharmcophore of pyrimethamine (2,4- diamino-5(4-chlorophenyl)-6-ethylpyrimidine), but encompassing a range of polar groups that might interact with the M. tuberculosis DHFR glycerol binding pockets. Finally, the research described in this thesis contributes to the preparation of molecularly imprinted polymers for the recognition of 2,4-diaminopyrimidine for the binding the target. The formation of hydrogen bonding between the model functional monomer 5-(4-tert-butyl-benzylidene)-pyrimidine-2,4,6-trione and 2,4-diaminopyrimidine in the pre-polymerisation stage was verified by 1H-NMR studies. Having proven that 2,4-diaminopyrimidine interacts strongly with the model 5-(4-tert-butylbenzylidene)- pyrimidine-2,4,6-trione, 2,4-diaminopyrimidine-imprinted polymers were prepared using a novel cyclobarbital derived functional monomer, acrylic acid 4-(2,4,6-trioxo-tetrahydro-pyrimidin-5- ylidenemethyl)phenyl ester, capable of multiple hydrogen bond formation with the 2,4- diaminopyrimidine. The recognition property of the respective polymers toward the template and other test compounds was evaluated by fluorescence. The results demonstrate that the polymers showed dose dependent enhancement of fluorescence emissions. In addition, the results also indicate that synthesized MIPs have higher 2,4-diaminopyrimidine binding ability as compared with corresponding non-imprinting polymers.

Structural studies on antifolate drugs

Single crystal X-ray structure determinations are reported for eleven compounds all of which are either biologically active or potentially biologically important. The compounds fall into two distinct classes:- 1. Substituted diaminopyrimidines 2. Substituted aminopyrimidinones The first class of compounds were all selected on the basis of their common diaminopyrimidine nucleus which has been demonstrated to be a vital requirement for antifolate activity. They may all be described as non-classical or small molecule lipophilic dihydrofolate reductase (DHFR) inhibitors, as opposed to the classical folate analogues, having the ability to cross the blood-brain barrier, enter cells via a rapid passive diffusion process, and achieve high intracellular concentrations. Thus they are an excellent choice in the search for crystallography in the solid state, providing geometrical and distance data not available from any other analytical techniques to date; supporting and enhancing data obtained in the lower resolution studies of protein crystallography. The biological importance of these compounds is discussed and an attempt is made to relate/predict their pharmacological activity to observed structural features in the crystalline environment. Special attention is focussed on hydrogen bonding, confirmational flexibility and hydrophobicity of substituents; each of which appear to make contributions to tight binding in the enzyme active site. Chapter 9 describes the use of data from the literature and the solid state modelling of an observed enzyme-substrate interaction in an attempt to define it more accurately in terms of its geometric flexibility. Of the second class, one compound (ABPP) is reported; studies in two different crystal forms. In demonstrating both antiviral and high interferon inducing activity it is possible that this compound could be useful against cancer and also viral infections.

Studies on DNA methylation and mechanisms of hypomethylation

The methylation of cytosinc residues in DNA is thought to play an important role in the regulation of gene expression, with active genes generally being hypomethylated. With this in mind peptides were synthcsised to mimic the cytosine-5 methylation activity carried out by DNA mcthylase, which however, showed no ability to carry out this function. The imidazotetrazinoncs are a novel group of antitumour agents which have demonstrated good activity against a range of murinc tumours and human tumour xenografts, and hypomethylation of DNA has been implicated in the mechanism of action. Studies have been conducted on the mechanism by which such agents cause hypomethylation, using DNA methylase partially purified from murine L1210 leukaemia cells. Unmodified calf thymus DNA does not inhibit the transfer of methyl groups from SAM to M.lysodeikticus DNA by partially purified DNA methylase. However, if the calf thymus DNA is modified by alkylating agents such as imida-zotetrazinones or nitrosoureas, the treated DNA becomes an inhibitor of the methylation reaction. This has been correlated with the induction of DNA damage, such as single strand breaks, since X-ray treated DNA and deoxyribonuclease treatment produces a similar effect. The mechanism of inhibition by the drug treated or damaged DNA is thought to occur by binding of the enzyme to an increased concentration of non-substrate DNA, presumably by the occurrence of single strand breaks, since neither sonication nor treatment with the restriction enzyme Mspl caused an inhibition. Attempts were made to elucidate the strict structure activity relationship for antitumour activity observed amongst the imidazotctrazinones. The transfection of a murine colon adcnocarcinoma cell line (MAC 13) with DNA extracted from GM892 or Raji cells previously treated with either the methyl (temozolomide) or ethyl (ethazolastone) imidazotetrazinone was performed. X-irradiated DNA did not cause any suppression of cell growth, suggesting that it was not due to physical damage. Transfection of MAC 13 cells with DNA extracted from GM892 cells, was more effective at inhibiting growth than DNA from Raji cells. Temozolomide treated cellular DNA was a more potent growth inhibitor than that from ethazolastone treated cells. For both agents the growth inhibitory effect was most marked with DNA extracted 6h after drug addition, and after 24h no growth suppression was observed. This suggested that the growth inhibitory effect is due to a repairable lesion. .The methylation of M.lysodeikticus DNA by DNA methylase is inhibited potently and specifically by both hereto and homoribo and dcoxyri-bopolynucleotides containing guanine residues. The inhibitory effect is unaffected by chain length or sugar residue, but is abolished when the O-6 residue of guanine is substituted as in poly d(OGG)2o. Potent inhibition is also shown by polyinosinic and polyxanthylic acids but not by polyadenylic acid or by heteropolymers containing adcnine and thymine. These results suggest that the 6 position of the purine nucleus is important in binding of the DNA methylase to particular regions of the DNA and that the hydrogen bonding properties of this group are important in enzyme recognition. This was confirmed using synthetic oligonucleotides as substrates for DNA methylase. Enzymatic methylation of cytosine is completely suppressed, when O6 methylguanine replaces guanine in CG sites.

Antitumour imidazotetrazines: probes for the major groove of DNA

The antitumour imidazotetrazinones are believed to act as prodrugs for the triazene series of alkylating agents, showing a marked pteference for the alkylation of the middle guanine residue in a run of three or more contiguous guanines. However, the. exact nature of the interactions of imidazotetrazinones within the micro~environment of DNA are; as yet unknown. In order to examine such interactions a three pronged approach involving molecular modelling, synthetic chemistry and biological analysis has been undertaken during the course of this project. . Molecular modelling studies have shown that for the 8-carboxamido substituted imidazotetrazinones antitumour activity is dependent upon the. presence of a free NH group which can be involved in the formation of both intramolecular and intermolecular hydrogen bonds, and the presence of a non-bulky substituent with a small negative potential . volume. Modelling studies involving the docking of .mitozolomide into the major groove of DNA in the region of a triguanine sequence has shown that a number of hydrogen bonding interactions are feasible. A series of 8-substituted carboxamide derivatives of mitozolomide have been synthesised via the 8-acid chloride and 8-carboxylic acid derivatives including a number of peptide analogues. The peptide derivatives were based upon the key structural features of the helix-turn-helix motif of DNA-binding proteins with a view to developing agents that are capable of binding to DNA with greater selectivity. An examination of the importance of intramolecular hydrogen bonding in influencing the antitumour activity:of :the imidazotetrazinones has led to the synthesis of the novel pyrimido[4',5' :4,3]pyrazolo[5,1-d]-1,2,3,5-tetrazine ring system. In general, in vitro cytotoxicity assays showed that the new derivatives were less active against the TLX5 lymphoma cell line. than the parent compound mitozolomide despite an increased potential for hydrogen bonding interactions. Due to the high reactivity of the: tetrazinone ring system it is difficult to study the interactions between the imidazotetrazinones and DNA. Consequently a number of structural analogues that are stable under physiological conditions have been. prepared based upon the 1,2,3 triazin-4(3H)-one ring system fused with both benzene and pyrazole rings. Although the 3-methylbenzotriazinones failed to antagonise the cytotoxic activity of temozolomide encouraging results with a 3-methylpyrazolotriazinone may suggest the existence of an imidazotetrazinone receptor site within DNA. The potential of guanine rich sequences to promote the alkylating selectivity of imidazotetrazinones by acting as a catalyst for ring cleavage and thereby generation of the alkylating agent was examined. Experiments involving the monitoring: of the rate of breakdown of mitozolomide incubated in the presence of synthetic oIigonucleotides did not reveal any catalytic effect resulting from the DNA. However, it was noted that the breakdown of mitozolomide was dependent upon the type of buffer used in the incubations and this may indeed mask any catalysis by the oligonucleotides.