Prodrug strategies of antiviral nucleotides: Studies on enzymatically and thermally removable phosphate protecting groups

Antiviral nucleosides are compounds that are used against viruses, such as human immunodeficiency virus (HIV) and hepatitis C virus (HCV). To act as therapeutic agent, the antiviral nucleoside needs to be phosphorylated to nucleotide in the body in three consecutive phosphorylation steps by cellular or viral enzymes. The first phosphorylation to the nucleoside monophosphate is often inefficient and leads to poor antiviral activity. The antiviral efficacy can be improved by applying a prodrug strategy and delivering the antiviral nucleoside directly as its monophosphate. In prodrug strategies of antiviral nucleotides, the negative charges on the phosphate moiety are temporarily masked with protecting groups. Once inside the cell, the protecting groups are removed by enzymatic or chemical processes. Many prodrug strategies apply biodegradable protecting groups, the removal of which is triggered by esterase enzymes. Several studies have, however, demonstrated that the removal rate of the second and subsequent esterase labile protecting groups significantly slows down after the first protecting group is removed due to the negative charge on the phosphodiester intermediate, which disturbs the catalytic site of the enzyme. In this thesis, esterase labile protecting group strategies where the issue of retardation could be avoided were studied. Prodrug candidates of antiviral nucleotides were synthesized and kinetic studies on the chemical and enzymatic stability were carried out. In the synthesized compounds, the second protecting group is cleaved from the monophosphate some other mechanism than esterase triggered activation or the structure of prodrug requires only one protecting group. In addition, esterase labile protecting group which is additionally thermally removable was studied. This protecting group was cleaved from oligomeric phosphodiesters both enzymatically and thermally and seems most attractive of the studied phosphate protecting groups. However, the rate of the thermal removal still is too slow to allow efficient protection of longer oligonucleotides and needs optimization. Key words: antiviral, nucleotide, prodrug, protecting group, biodegradable

Puristussylinterien valmistuksen kehittäminen

Tässä diplomityössä kehitettiin yksitoimisten puristussylinterien valmistusta Rautessa. Sylinterien valmistuksessa haastavin vaihe on sylinteriputken ja pohjan välinen hitsaus. Hitsauksen avuksi suunniteltiin sylinterin sisäpuolinen juuritukilaite. Hitsauskokeita suoritettiin hitsin pohjan jauhekaarihitsaukselle ja MAG-hitsaukselle. Juuritukilaitteen toimivuutta testattiin koehitsauksilla. Puristussylinterien materiaali on S355J2-terästä, jonka ainevahvuus on 20 – 60 mm. Paksujen rakenneterästen hitsauksessa täytyy ottaa huomioon hitsausliitoksen mekaanisten ominaisuuksien muuttuminen sekä eri halkeamien synty. Hitsauksen laatuun ja laadunhallintaan voidaan vaikuttaa monien eri tekijöiden avulla. Hitsausohjeen avulla, ja muut laatutekijät huomioiden, voidaan hitseille asetetut laatukriteerit täyttää. Juurituen käyttö nopeuttaa puristussylinterien hitsausta vähintään 50 %. Jauhekaarihitsaus kuparista juuritukea vasten synnyttää vaikeasti poistettavan kuonan juuren puolelle. Perinteinen MAG-hitsaus kuparista juuritukea vasten sisältää liian monta muuttujaa, mikä tekee siitä epäluotettavan pohjapalon hitsaukseen. Työssä suunnitellun juuritukilaitteen käyttö tuotannossa vaatii lisää hitsauskokeita.

Use of fiber-reinforced composite framework and thermochromic pigment in maxillofacial prostheses

The purpose of this investigation was to evaluate the possibility to enhance certain qualities of facial prostheses. Polymethyl methacrylate is still being used as base mate¬rial or clip carrier material, but it is hard and heavy, and debonding of the silicone from the acrylic base material is a frequent problem. This thesis aims to evaluate the use of fiber-reinforced composite (FRC) as framework material for maxillofacial silicone prostheses. FRC has been used as reinforcement in removable and fixed partial dentures since the 1990s. This material is lightweight and can be fabricated to compress the margins of the prosthesis slightly, to keep it tightly against the skin during jaw movements and facial expressions. Additionally, the use of a thermochromic pigment, colorless in room temperature and red in a cold environment, was studied in order to evaluate the possibility of using this color changing pigment in facial prostheses to mimic the color change of facial skin in cold weather. The tensile bond strength between pre-impregnated, unidirectional FRC and maxillofacial silicone elastomer was studied. Three different bonding agents or primers were compared. Bond strength was improved by one of the primers and by roughening the surface. The effect of a skin compressing glass fiber-reinforced composite framework on facial skin blood flow was studied by using a face mask, constructed with a compression pad corresponding to the outer margin of a glass fiber-reinforced framework beam of a facial prosthesis. The skin blood flow of ten healthy volunteers, aged 23-25 years, was measured during touch, light, and moderate compression of the skin, by using laser Doppler imaging technique. None of the compressions showed any marked effects on local skin blood flow. There were no significant differences between blood flow during compression and at baseline. Maxillofacial silicone elastomer was colored intrinsically with conventional color pigments: a control group containing only conventional pigments was compared to two test groups with 0.2 wt% and 0.6 wt% thermochromic pigment added. The color of the material was measured with a spectrophotometer in room temperature and after storage in a freezer. The color stability of the maxillofacial silicone elastomer colored with thermo¬chromic pigment was evaluated by artificial aging. The color dif¬ference of the L* (lightness) and a* values (redness), comparing color after the samples were stored at room temperature and in a freezer (-19°C), was statistically significant for both 0.2 wt% and 0.6 wt% thermo¬chromic pigment groups. The differences in the b* values (yellowness) were statistically significant for the 0.6 wt% group. Exposure to ultraviolet (UV) radiation led to visually noticeable and statistically signifi¬cant color changes (ΔE) in all color values in both test groups. The specimens containing thermochromic pigment were very sensitive to UV radiation. In conclusion, a framework of fiber-reinforced composite can successfully be bonded to maxillofacial silicone elastomer, and a framework beam, compressing the facial skin, did not remarkably alter the skin blood flow on healthy, young adults. The thermochromic pigment showed color change in maxillofacial silicone elastomer. However, artificial aging showed that it was too sensitive to UV radiation to be used, as such, in maxillofacial prostheses.

Synthesis of Short Oligonucleotides on a Soluble Support by the Phosphoramidite Method

In the last decades, the chemical synthesis of short oligonucleotides has become an important aspect of study due to the discovery of new functions for nucleic acids such as antisense oligonucleotides (ASOs), aptamers, DNAzymes, microRNA (miRNA) and small interfering RNA (siRNA). The applications in modern therapies and fundamental medicine on the treatment of different cancer diseases, viral infections and genetic disorders has established the necessity to develop scalable methods for their cheaper and easier industrial manufacture. While small scale solid-phase oligonucleotide synthesis is the method of choice in the field, various challenges still remain associated with the production of short DNA and RNA-oligomers in very large quantities. On the other hand, solution phase synthesis of oligonucleotides offers a more predictable scaling-up of the synthesis and is amenable to standard industrial manufacture techniques. In the present thesis, various protocols for the synthesis of short DNA and RNA oligomers have been studied on a peracetylated and methylated β-cyclodextrin, and also on a pentaerythritol-derived support. On using the peracetylated and methylated β-cyclodextrin soluble supports, the coupling cycle was simplified by replacement of the typical 5′-O-(4,4′-dimethoxytrityl) protecting group with an acid-labile acetal-protected 5′-O-(1-methoxy-1-methylethyl) group, which upon acid-catalyzed methanolysis released easily removable volatile products. For this reason monomeric building blocks 5′-O-(1-methoxy-1-methylethyl) 3′-(2-cyano-ethyl-N,N-diisopropylphosphoramidite) were synthesized. Alternatively, on using the precipitative pentaerythritol support, novel 2´-O-(2-cyanoethyl)-5´-O-(1-methoxy-1-methylethyl) protected phosphoramidite building blocks for RNA synthesis have been prepared and their applicability by the synthesis of a pentamer was demonstrated. Similarly, a method for the preparation of short RNAs from commercially available 5´-O-(4,4´-dimethoxytrityl)-2´-O-(tert-butyldimethyl-silyl)ribonucleoside 3´-(2-cyanoethyl-N,N-diisopropylphosphoramidite) building blocks has been developed