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Hepatitis C is a blood-borne disease affecting 130-170 million people worldwide. The causative agent, hepatitis C virus (HCV), infects the liver and is the major reason for chronic liver disease worldwide. The HCV NS3 protease, a key enzyme in the virus replication cycle, has been confirmed to be an important target for drug development. With the recent release of two HCV NS3 protease inhibitors onto the market and an arsenal of inhibitors in clinical trials, there are now hopes of finally combating the disease. However, the success of treatment relies heavily on the ability to overcome the emergence of drug-resistant forms of the protease. The main focus of this thesis was on designing and synthesizing novel inhibitors of the NS3 protease with a unique resistance profile. Efforts were also made to decrease the peptide character of the compounds, with the long-term goal of making them into more drug-like compounds. Special attention was devoted to developing inhibitors based on a phenylglycine in the P2 position, instead of the highly optimized and commonly used P2 proline. Around ninety acyclic and macrocyclic inhibitors have been synthesized and biochemically evaluated. P2 pyrimidinyloxy phenylglycine was successfully combined with an aromatic P1 moiety and alkenylic P1´ elongations, yielding a distinct class of HCV NS3 protease inhibitors. Macrocyclization was performed in several directions of the inhibitors via ring-closing metathesis. Only the macrocyclization between the P3-P1´ residues was successful in terms of inhibitory potency, which suggests that the elongated P1-P1´ residue is oriented towards the P3 side chain. The metathesis reaction was found to be significantly more dependent on the substrate than on the reaction conditions. It was also found that the P3 truncated inhibitors were able to retain good inhibitory potency, which initiated the synthesis and evaluation of a series of P2-P1´ inhibitors. The potential of the P3-P1´cyclized inhibitor and the smaller, acyclic P2-P1´ as new potential drug leads remains to be determined through pharmacokinetic profiling. Gratifyingly, all the inhibitors evaluated on A156T and D168V substituted enzyme variants were able to retain inhibitory potency towards these as compared to wild-type inhibition.

Infection by the hepatitis C virus (HCV) leads to inflammation of the liver, i.e. hepatitis. The acute infection often progresses to a chronic phase during which the liver function is gradually impaired. Approximately 20% of these chronic cases develop liver cirrhosis, with an ensuing increased risk of liver cancer. Global estimates of the total number of chronic cases range from 123–170 million. Yet, neither specific anti-HCV drugs nor vaccines are available. When drugs become available for daily clinical use, rapid development of drug-resistant strains is expected, making resistance an important issue. One of the most studied targets for specific anti-HCV drugs is the NS3 protease. The main objectives of the work presented in this thesis were to design and synthesise peptidomimetic inhibitors of this enzyme, and to establish the structure–activity relationships (SARs) regarding the inhibition of the wild type as well as of the known resistant variants A156T and D168V. Substituted prolines are common P2 residues in HCV NS3 protease inhibitors. To decrease the peptide character of the inhibitors, the non-coded phenylglycine was evaluated as a proline replacement in combination with known and novel P3 and P1 residues and P2 substituents. The results confirmed that phenylglycine is a promising P2 scaffold, with a possible π-stacking interaction with histidine 57 of the active site. However, to benefit from its full potential, additional optimisation is required. A 2(1H)-pyrazinone-based scaffold was introduced as P3 residue. Utilising the scope of the method developed for the pyrazinone scaffold synthesis, the phenylglycine side-chain was transferred to the scaffold. In combination with an aromatic P1 building-block, this design yielded achiral, peptidomimetic inhibitors, three times more potent than the tripeptide lead. The SARs for the inhibition of the resistant variants A156T and D168V were investigated for compounds based on either P2 proline or phenyl­glycine. It was concluded that the vulnerability of the inhibitors to alterations in the enzyme depends on the P2 and the P1 residue, not only on the P2 as previously suggested. These results provide important information for the design of a new generation of inhibitors with improved properties.

Made available in DSpace on 2016-08-17T18:39:31Z (GMT). No. of bitstreams: 1 2631.pdf: 1610800 bytes, checksum: 9f443d37247fb5fee135a70ec93a8142 (MD5) Previous issue date: 2008-09-29 / Financiadora de Estudos e Projetos / Immobilization and stabilization of enzymes increases their potential for use in industrial scale. D-hydantoinases (dihidropirimidina amidrohidrolase EC 3.5.2.2) catalyze the hydrolysis of D-hydantoins, generating the corresponding Ncarbamoil- D-amino acid and are used in the production of D-amino acids, including Dphenylglycine and D-p-hydroxyphenylglycine.This work reports studies for immobilization and stabilization of D-hydantoinase from Vigna angularis (E.C. 3.5.2.2.). Different strategies of multipoint covalent attachment in organic supports as chitosan and agarose were used. Different protocols of immobilization were employed, being the adittion of ions during the reduction step with the NaBH4 important to protect enzyme catalytic site. The active and stabilized derivatives were used to catalyze the hydrolysis of D-phenylhydantoin. The temperature and pH enzyme profiles showed maximum enzyme activity at 60ºC and pH 10,0. The subunits of the enzyme present molecular mass aroundt 50kDa. The enzyme immobilized in glyoxyl-agarose in the presence of Zn2+ ions during the reduction step, with immobilization time of 24h, was the best derivative, being 89-fold more stable than the soluble enzyme. The analysis of amino acids showed that a 50% of lysines residue present in the enzymes was covalently linked in glyoxyl-agarose. The enzyme immobilized in epoxy-chitosan-alginate was 20-fold more stable than the soluble enzyme. All the tested immobilization protocols led to 100% of immobilization yield. Soluble enzyme and the best glyoxyl and chitosan enzyme derivatives were used to catalyze the hydrolysis of D- phenylhydantoin , and led to the production of 99% of NCarbamoil- D-Phenylglycine after 3, 9 and 15h of reaction respectively. / A imobilização e estabilização de enzimas aumentam muito o potencial de uso industrial desses catalisadores. D-hidantoinases (dihidropirimidina amidrohidrolase EC 3.5.2.2) são enzimas que catalisam a hidrólise de hidantoínas, com abertura do anel, para o correspondente N-carbamoil-D-aminoácido e são usadas na produção de Daminoácidos, incluindo D-fenilglicina e D-p-hidroxifenilglicina. Este trabalho relata os estudos desenvolvidos para a imobilização e estabilização de D-hidantoinase de Vigna angularis (3.5.2.2.). Foram abordadas diferentes estratégias de imobilização multipontual em suportes orgânicos como quitosana e agarose. Diferentes protocolos de imobilização foram empregados, sendo adição de íons durante a redução com NaBH4 importante para proteção do centro catalítico da enzima. Os derivados ativos e estabilizados foram empregados na reação de hidrólise da fenilhidantoína. O estudo de temperatura e pH de máxima atividade da enzima foi 60°C e pH 10,0. As subunidades da enzima apresentam peso molecular, com valor próximo a 50kDa. A enzima imobilizada em glioxil-agarose na presença dos íons Zn2+ durante a etapa de redução, com tempo de imobilização de 24 h foi o derivado mais estável sendo 89 vezes mais estável que a enzima solúvel. A análise de aminoácidos mostrou que aproximadamente 50% dos resíduos de lisina presentes na enzima foram covalentemente ligados no derivado de glioxil-agarose. A enzima imobilizada em quitosana-alginato-epoxilado foi 20 vezes mais estável que a enzima solúvel. Todos os procedimentos de imobilização testados levaram a 100% de rendimento de imobilização. Enzima solúvel e os melhores derivados obtidos por imobilização em glioxil e quitosana foram usados na catálise da hidrólise de fenilhidantoína, produzindo 99% de N-Carbamoil-D-fenilglicina nos tempos de 3, 9 e 15 h, respectivamente.