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Search for New Antiviral Compounds Using Fragment Screening Methodology

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Search for New Antiviral Compounds Using Fragment Screening Methodology Search for new antiviral compounds using fragment screening methodology Zuzanna Kaczmarska Aquesta tesi doctoral està subjecta a la llicència Reconeixement 3.0. Espanya de Creative Commons. Esta tesis doctoral está sujeta a la licencia Reconocimiento 3.0. España de Creative Commons. This doctoral thesis is licensed under the Creative Commons Attribution 3.0. Spain License. Facultat de Farmàcia Departament de Bioquímica i Biologia Molecular Search for new antiviral compounds using fragment screening methodology Zuzanna Kaczmarska Barcelona, 2014 Thesis submitted by Zuzanna Kaczmarska, enrolled in the Biotechnology program at the University of Barcelona, for the degree of Doctor of Philosophy. This work was carried out in the Structural Biology of Protein & Nucleic Acid Complexes and Molecular Machines Group at the Institute for Research in Biomedicine (IRB-Barcelona) and Molecular Biology Institute of Barcelona (IBMB-CSIC), under the supervision of Prof. Miquel Coll Capella. Zuzanna Kaczmarska Miquel Coll Capella IRB Barcelona IRB Barcelona IBMB-CSIC IBMB-CSIC Barcelona, 2014 Preface Picornaviridae are among the most diverse and oldest known viral families that include many important pathogens of humans and animals. They are small, icosahedral (+)ssRNA viruses, causing a variety of diseases, such as encephalitis, and poliomyelitis. Vaccines are available for poliovirus, hepatitis A virus and foot and mouth disease virus, but no effective prophylaxis is implemented for other picornaviruses. Thus far, anti-viral research has focused on the capsid, whereas inhibitors targeting non-structural proteins (i.e. proteases, helicases, polymerases) have remained largely unaddressed. The project was focused on structural and biochemical characterization of the enterovirus-B93 (EV-B93) 3C protease alone and in complex with several covalent inhibitors. The second objective was to identify the first non-covalent potent inhibitors of the EV-B93 3C protease and their further biochemical, antiviral, and structural evaluation. 5 List of abbreviations and symbols # number °C degree Celsius ΔG Gibbs energy [v/v] volume per volume [w/v] weight per volume 1,8-ANS 1-anilinonaphthalene- 8-sulfonic acid 2,6-TNS 2-p-toluidinyl-6-naphthalene sulfonate 3D three dimensions 3CL protease 3C-like protease 5’UTR 5’ untranslated region Å Angstrom ADMET absorption, distribution, metabolism, secretion, toxicity Ac acetyl AiV aichi virus APS ammonium persulfate ATP adenosine-5’-triphosphate C-terminal carboxy-terminal Cbz carboxybenzyl CDK2 cyclin-dependent kinase 2 clogP calculated logP CoV coronavirus CPE cytopathic effect CV column volume, coxsackievirus Da Dalton DMAB dimethylaminoborane DMSO dimethylsulphoxide DNA deoxyribonucleic acid DSS 4,4-dimethyl-4-silapentane-1-sulfonic acid DTT dithiothreitol EC50 half maximal effective concentration EDC 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide ERAV equine rhinitis A virus ERBV equine rhinitis B virus EV enterovirus FABP4 fatty acid binding protein 4 FBDD fragment-based drug design FDA Food and Drug Administration FMDV Foot-and-mouth disease g gram GAL4BD GAL4 binding domain h hour 6 HAV hepatitis A virus HEPES 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid His-tag poly(6) histidine-tag HPLC high performance/pressure liquid chromatography HRV human rhinovirus HSQC heteronuclear single quantum correlation HTS high-throughput screening Hz hertz IC50 half maximal inhibitory concentration IMAC immobilized metal ion affinity chromatography IRES internal ribosomal entry k kilo (103) Kd dissociation constant Ki inhibitory constant koff dissociation rate constant l liter LB Luria-Bertani LE ligand efficiency μ micro (10-6) M molar, marker m mili (10-3) m/z mass-to-charge ratio MALDI-TOF matrix-assisted laser desorption/ionization time-of-flight MD molecular dynamics min minute MPD 2-methyl-2,4-pentanediol MS mass spectrometry MTT 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide MW molecular weight MWCO molecular weight cut-off n nano (10-9) N-terminal amino-terminal Ni-NTA nickel-nitrilotriacetic acid NHS N-hydroxysuccinimide NMR nuclear magnetic resonance NROT number of rotational bonds P partition coefficient between octanol and water PAGE polyacrylamide gel PDB protein data bank PCR polymerase chain reaction PEG polyethylene glycol ppm parts per million PSA polar surface area PSV porcine sapelovirus 7 PV poliovirus RA relative activity RLU relative light unit RMSD root mean square deviation RNA ribonucleic acid RPC reverse phase chromatography rpm revolutions per minute RU response unit RV rhinovirus s second S/N signal-to-noise ratio SAR structure-activity relationship SARS severe acute respiratory syndrome SDS sodium dodecyl sulfate SPR surface plasmon resonance (+)ssRNA positive single-stranded RNA STD saturation transfer difference TEMED N,N,N,N-tetramethylendiamine TFA trifluoroacetic acid TINS target immobilized NMR screening Tm melting temperature Tris Tris(hydroxymethyl)aminomethane TSA thermal shift assay V Volt VP16AD VP16 activation domain 8 Amino acids abbreviations 1-letter code 3-letter code amino acid A Ala alanine R Arg arginine N Asn asparagine D Asp aspartic acid C Cys cysteine E Glu glutamic acid Q Gln glutamine G Gly glycine H His histidine I Ile isoleucine L Leu leucine K Lys lysine M Met methionine F Phe phenylalanine P Pro proline S Ser serine T Thr threonine W Try tryptophan Y Tyr tyrosine V Val valine 9 Table of contents Preface ..................................................................................................................................... 5 List of abbreviations and symbols ............................................................................................. 6 Amino acids abbreviations ....................................................................................................... 9 Table of contents ................................................................................................................... 10 1. Introduction ...................................................................................................................... 15 1.1 Drug discovery ............................................................................................................. 17 1.1.1 Fragment-based drug discovery vs. high-throughput screening: a matter of chemical space ............................................................................................................................... 17 1.1.2 What is a fragment? ............................................................................................... 19 1.1.3 The drug-like molecule .......................................................................................... 19 1.1.4 Hit selection and lead optimization ....................................................................... 20 1.1.5 Detection of fragment binding .............................................................................. 21 1.1.5.1 Nuclear Magnetic Resonance .......................................................................... 22 1.1.5.2 Surface plasmon resonance .............................................................................. 22 1.1.5.3 X-ray crystallography ...................................................................................... 23 1.1.5.4 Fluorescence melting assay .............................................................................. 23 1.1.5.5 Other methods ................................................................................................ 24 1.1.6 Elaboration of fragment hits .................................................................................. 24 1.2 Enteroviruses as a part of Picronaviridae family ............................................................ 26 1.2.1 Viral proteins ......................................................................................................... 27 1.2.2 3C protease ........................................................................................................... 29 1.2.3 Drugs targeting the 3C protease ............................................................................ 30 1.2.3.1 Peptidic inhibitors .......................................................................................... 31 1.2.3.1.1 Peptide aldehydes and ketones ................................................................. 31 1.2.3.1.2 Michael-acceptor-based inhibitors ............................................................ 32 1.2.3.1.3 Other peptidic inhibitors .......................................................................... 35 1.2.3.2 Non-peptidic inhibitors .................................................................................. 35 1.2.3.3 Non-covalent inhibitors .................................................................................. 39 10 2. Objectives .......................................................................................................................... 41 3. Materials and methods ....................................................................................................... 45 3.1 Materials ...................................................................................................................... 47 3.1.1 Expression vector ................................................................................................... 47 3.1.2 Plasmid purification .............................................................................................
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