Objev, návrh a charakterizace nových nepeptidových inhibitorů HIV-1 proteázy

Ph.D. thesis abstract Overcoming drug resistance : The discovery, design and characterization of new nonpeptidic inhibitors of HIV-1 protease Milan Kožíšek, M.Sc. Supervisor : Jan Konvalinka, Ph.D. PPrraagguuee 22001100 Department of Biochemistry Faculty of Science Charles University, Prague, Czech Republic Institute of Organic Chemistry and Biochemistry Gilead Sciences & IOCB Research Centre Academy of Sciences of the Czech Republic 3 Abstract HIV-1 protease is an aspartic protease which plays an essential role in the life cycle of HIV virus. It is responsible for the cleavage of the viral polyproteins into the structural and functional proteins during viral maturation. The efficient inhibition of the protease thus leads to the formation of immature and non-infectious viral particles. The introduction of protease inhibitors dramatically changed the treatment of retroviral infection. The viral replication was reduced to undetectable level and the rate of disease progression was significantly lowered. However, resistance to the inhibitors was observed. The first inhibitors had limited bioavailability, caused severe side effects and easily developed resistance. To combat these negative factors, second-generation inhibitors have been developed. Understanding the mechanisms of resistance toward inhibitors is...Doktorská dizertační práce - abstrakt Objev, návrh a charakterizace nových nepeptidových inhibitorů HIV-1 proteázy RNDr. Milan Kožíšek Školitel : Doc. RNDr. Jan Konvalinka, CSc. PPrraahhaa 22001100 Katedra biochemie Přírodovědecká fakulta Karlova univerzita, Praha, Česká republika Ústav organické chemie a biochemie Gilead Sciences & IOCB Research Centre Akademie věd České republiky 3 Abstrakt HIV-1 proteáza je aspártátová proteáza, jejíž aktivita je nezbytná v životním cyklu viru HIV. Je odpovědná za štěpení virových polyproteinů na strukturní proteiny a enzymy během zrání viru. Inhibice tohoto enzymu vede k tvorbě nezralých a tedy neinfekčních virových částic. Uvedení proteázových inhibitorů na trh dramaticky změnilo úspěch léčby retrovirové infekce. Množství viru v krevní plazmě pokleslo pod zjistitelnou úroveň a vývoj nemoci se výrazně zpomalil. Nicméně se začala vyvíjet rezistence k inhibitorům. První proteázové inhibitory vykazovaly nízkou biodostupnost, měly řadu nežádoucích účinků a snadno k nim byla vyvíjena rezistence. Aby se předešlo těmto nežádoucím jevům, byly a jsou stále vyvíjeny inhibitory druhé generace. Pochopení mechanismu, kterým rezistence vůči určitému inhibitoru vzniká, je velmi důležité při vývoji nových antiretrovirotik i při klinické léčbě. Kvůli vznikající rezistenci je stále nutné...Department of BiochemistryKatedra biochemieFaculty of SciencePřírodovědecká fakult

{2-[(S)-({2-[(S)-1-Benzyl­pyrrolidine-2-carboxamido]phen­yl}(phen­yl)methyl­ene)amino]-4-hydroxy­butanoato-κ4 N,N′,N′′,O}nickel(II)

The central Ni atom of the title compound, [Ni(C29H29N3O4)], is coordinated by three N atoms [Ni—N = 1.955 (2), 1.844 (2) and 1.872 (2) Å] and by one O atom [Ni—O = 1.862 (2) Å] in a pseudo-square-planar geometry. The conformation of the hydroxy­butanoate side chain is controlled by a strong intra­molecular hydrogen bond (H⋯O = 1.84 Å)

Overcoming drug resistance: The discovery, design and characterization of new nonpeptidic inhibitors of HIV - 1 protease

Ph.D. thesis abstract Overcoming drug resistance : The discovery, design and characterization of new nonpeptidic inhibitors of HIV-1 protease Milan Kožíšek, M.Sc. Supervisor : Jan Konvalinka, Ph.D. PPrraagguuee 22001100 Department of Biochemistry Faculty of Science Charles University, Prague, Czech Republic Institute of Organic Chemistry and Biochemistry Gilead Sciences & IOCB Research Centre Academy of Sciences of the Czech Republic 3 Abstract HIV-1 protease is an aspartic protease which plays an essential role in the life cycle of HIV virus. It is responsible for the cleavage of the viral polyproteins into the structural and functional proteins during viral maturation. The efficient inhibition of the protease thus leads to the formation of immature and non-infectious viral particles. The introduction of protease inhibitors dramatically changed the treatment of retroviral infection. The viral replication was reduced to undetectable level and the rate of disease progression was significantly lowered. However, resistance to the inhibitors was observed. The first inhibitors had limited bioavailability, caused severe side effects and easily developed resistance. To combat these negative factors, second-generation inhibitors have been developed. Understanding the mechanisms of resistance toward inhibitors is..

Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase

Influenza A virus (IAV) encodes a polymerase composed of three subunits: PA, with endonuclease activity, PB1 with polymerase activity and PB2 with host RNA five-prime cap binding site. Their cooperation and stepwise activation include a process called cap-snatching, which is a crucial step in the IAV life cycle. Reproduction of IAV can be blocked by disrupting the interaction between the PB2 domain and the five-prime cap. An inhibitor of this interaction called pimodivir (VX-787) recently entered the third phase of clinical trial; however, several mutations in PB2 that cause resistance to pimodivir were observed. First major mutation, F404Y, causing resistance was identified during preclinical testing, next the mutation M431I was identified in patients during the second phase of clinical trials. The mutation H357N was identified during testing of IAV strains at Centers for Disease Control and Prevention. We set out to provide a structural and thermodynamic analysis of the interactions between cap-binding domain of PB2 wild-type and PB2 variants bearing these mutations and pimodivir. Here we present four crystal structures of PB2-WT, PB2-F404Y, PB2-M431I and PB2-H357N in complex with pimodivir. We have thermodynamically analysed all PB2 variants and proposed the effect of these mutations on thermodynamic parameters of these interactions and pimodivir resistance development. These data will contribute to understanding the effect of these missense mutations to the resistance development and help to design next generation inhibitors

Molecular Characterization of Clinical Isolates of Human Immunodeficiency Virus Resistant to the Protease Inhibitor Darunavir ▿ †

Darunavir is the most recently approved human immunodeficiency virus (HIV) protease (PR) inhibitor (PI) and is active against many HIV type 1 PR variants resistant to earlier-generation PIs. Darunavir shows a high genetic barrier to resistance development, and virus strains with lower sensitivity to darunavir have a higher number of PI resistance-associated mutations than viruses resistant to other PIs. In this work, we have enzymologically and structurally characterized a number of highly mutated clinically derived PRs with high levels of phenotypic resistance to darunavir. With 18 to 21 amino acid residue changes, the PR variants studied in this work are the most highly mutated HIV PR species ever studied by means of enzyme kinetics and X-ray crystallography. The recombinant proteins showed major defects in substrate binding, while the substrate turnover was less affected. Remarkably, the overall catalytic efficiency of the recombinant PRs (5% that of the wild-type enzyme) is still sufficient to support polyprotein processing and particle maturation in the corresponding viruses. The X-ray structures of drug-resistant PRs complexed with darunavir suggest that the impaired inhibitor binding could be explained by change in the PR-inhibitor hydrogen bond pattern in the P2′ binding pocket due to a substantial shift of the aminophenyl moiety of the inhibitor. Recombinant virus phenotypic characterization, enzyme kinetics, and X-ray structural analysis thus help to explain darunavir resistance development in HIV-positive patients

Dispersion interactions govern the strong thermal stability of a protein

Rubredoxin from the hyperthermophile Pyrococcus furiosus (Pf Rd) is an extremely thermostable protein, which makes it an attractive subject of protein folding and stability studies. A fundamental question arises as to what the reason for such extreme stability is and how it can be elucidated from a complex set of interatomic interactions, We addressed this issue first theoretically through a computational analysis of the hydrophobic core of the protein and its mutants, including the interactions taking place inside the core, Here we show that a single mutation of one of phenylalanine\u27s residues inside the protein\u27s hydrophobic core results in a dramatic decrease in its thermal stability. The calculated unfolding Gibbs energy as well as the stabilization energy differences between a few core residues follows the same trend as the melting temperature of protein variants determined experimentally by microcalorimetry measurements. NMR spectroscopy experiments have shown that the only part of the protein affected by mutation is the reasonably rearranged hydrophobic core. It is hence concluded that stabilization energies, which are dominated by London dispersion, represent the main source of stability of this protein. © 2007 Wiley-VCH Verlag GmbH & Co. KGaA,

[2-((R)-{2-[(S)-1-Benzylpyrrolidin-2-yl-carbonylazanidyl]phenyl}(phenyl)methylideneamino)-4-hydroxybutanoato-kappa(4)N,N ',N '',O(1)]nickel(II) toluene disolvate

The central Ni atom in the title compound, [Ni(C29H 29N3O4)]·2C7H8, is coordinated in a distorted squareplanar environment by three N atoms [Ni - N = 1.942 (3), 1.843 (3) and 1.853 (3) Å] and one O atom [1.868 (3) Å] of the tetradentate ligand. The conformation of the hydroxybutanoate side chain is controlled by an intermolecular hydrogen bond