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Daniel Schlatter,
Simon Brack,
David W Banner,
Sarah Batey,
Jörg Benz,
Julian Bertschinger, Walter Huber,
Catherine Joseph,
Arne Rufer,
Anita van der Klooster,
Martin Weber,
Dragan Grabulovski,
Michael Hennig
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ABSTRACT: The serine protease chymase (EC = 3.4.21.39) is expressed in the secretory granules of mast cells, which are important in allergic reactions. Fynomers, which are binding proteins derived from the Fyn SH3 domain, were generated against human chymase to produce binding partners to facilitate crystallization, structure determination and structure-based drug discovery, and to provide inhibitors of chymase for therapeutic applications. The best Fynomer was found to bind chymase with a KD of 0.9 nM and koff of 6.6x10 (-4) s (-1) , and to selectively inhibit chymase activity with an IC 50 value of 2 nM. Three different Fynomers were co-crystallized with chymase in 6 different crystal forms overall, with diffraction quality in the range of 2.25 to 1.4 Å resolution, which is suitable for drug design efforts. The X-ray structures show that all Fynomers bind to the active site of chymase. The conserved residues Arg15-Trp16-Thr17 in the RT-loop of the chymase binding Fynomers provide a tight interaction, with Trp16 pointing deep into the S1 pocket of chymase. These results confirm the suitability of Fynomers as research tools to facilitate protein crystallization, as well as for the development of assays to investigate the biological mechanism of targets. Finally, their highly specific inhibitory activity and favorable molecular properties support the use of Fynomers as potential therapeutic agents.
mAbs 07/2012; 4(4):497-508.
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ABSTRACT: Over the past decade, fragment-based drug discovery (FBDD) has gained importance for the generation of novel ideas to inspire synthetic chemistry. In order to identify small molecules that bind to a target protein, multiple approaches have been utilized by various groups in the pharmaceutical industry and by academic groups. The combination of fragment screening by biophysical methods and in particular with surface plasmon resonance technologies (SPR) together with the visualization of the binding properties by X-ray crystallography offers a number of benefits. Screening by SPR identifies ligands for a target protein as well as provides an assessment of the binding properties with respect to affinity, stoichiometry, and specificity of the interaction. Despite the huge technology advances of the past years, X-ray crystallography is still a resource-intensive technology, and SPR binding data provides excellent measures to prioritize X-ray experiments and consequently enable a better success rate in obtaining structural information. Information on the chemical structures of fragments binding to a protein can be used to perform similarity searches in compound libraries in order to establish structure-activity relationships as well as to explore particular scaffolds. At Roche we have applied this workflow for a number of targets and the experiences will be outlined in this review.
Topics in current chemistry 08/2011; 317:115-43. · 4.29 Impact Factor
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Eric J Niesor,
Christine Magg,
Naoto Ogawa,
Hiroshi Okamoto,
Elisabeth von der Mark,
Hugues Matile,
Georg Schmid,
Roger G Clerc,
Evelyne Chaput,
Denise Blum-Kaelin, Walter Huber,
Ralf Thoma,
Philippe Pflieger,
Makoto Kakutani,
Daisuke Takahashi,
Gregor Dernick,
Cyrille Maugeais
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ABSTRACT: The mechanism by which cholesteryl ester transfer protein (CETP) activity affects HDL metabolism was investigated using agents that selectively target CETP (dalcetrapib, torcetrapib, anacetrapib). In contrast with torcetrapib and anacetrapib, dalcetrapib requires cysteine 13 to decrease CETP activity, measured as transfer of cholesteryl ester (CE) from HDL to LDL, and does not affect transfer of CE from HDL3 to HDL2. Only dalcetrapib induced a conformational change in CETP, when added to human plasma in vitro, also observed in vivo and correlated with CETP activity. CETP-induced pre-β-HDL formation in vitro in human plasma was unchanged by dalcetrapib ≤3 µM and increased at 10 µM. A dose-dependent inhibition of pre-β-HDL formation by torcetrapib and anacetrapib (0.1 to 10 µM) suggested that dalcetrapib modulates CETP activity. In hamsters injected with [³H]cholesterol-labeled autologous macrophages, and given dalcetrapib (100 mg twice daily), torcetrapib [30 mg once daily (QD)], or anacetrapib (30 mg QD), only dalcetrapib significantly increased fecal elimination of both [³H]neutral sterols and [³H]bile acids, whereas all compounds increased plasma HDL-[³H]cholesterol. These data suggest that modulation of CETP activity by dalcetrapib does not inhibit CETP-induced pre-β-HDL formation, which may be required to increase reverse cholesterol transport.
The Journal of Lipid Research 12/2010; 51(12):3443-54. · 5.56 Impact Factor
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Lilli Anselm,
David W Banner,
Jörg Benz,
Katrin Groebke Zbinden,
Jacques Himber,
Hans Hilpert, Walter Huber,
Bernd Kuhn,
Jean-Luc Mary,
Michael B Otteneder,
Narendra Panday,
Fabienne Ricklin,
Martin Stahl,
Stefan Thomi,
Wolfgang Haap
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ABSTRACT: A series of (3R,4R)-pyrrolidine-3,4-dicarboxylic acid amides was investigated with respect to their factor Xa inhibitory activity, selectivity, pharmacokinetic properties, and ex vivo antithrombotic activity. The clinical candidate from this series, R1663, exhibits excellent selectivity against a panel of serine proteases and good pharmacokinetic properties in rats and monkeys. A Phase I clinical study with R1663 has been finalized.
Bioorganic & medicinal chemistry letters 09/2010; 20(17):5313-9. · 2.65 Impact Factor
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Eric Kitas,
Peter Mohr,
Bernd Kuhn,
Paul Hebeisen,
Hans Peter Wessel,
Wolfgang Haap,
Armin Ruf,
Jörg Benz,
Catherine Joseph, Walter Huber,
Ruben Alvarez Sanchez,
Axel Paehler,
Agnes Benardeau,
Marcel Gubler,
Brigitte Schott,
Effie Tozzo
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ABSTRACT: Sulfonylureido thiazoles were identified from a HTS campaign and optimized through a combination of structure-activity studies, X-ray crystallography and molecular modeling to yield potent inhibitors of fructose-1,6-bisphosphatase. Compound 12 showed favorable ADME properties, for example, F=70%, and a robust 32% glucose reduction in the acute db/db mouse model for Type-2 diabetes.
Bioorganic & medicinal chemistry letters 11/2009; 20(2):594-9. · 2.65 Impact Factor
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ABSTRACT: Surface plasmon resonance (SPR) technology has emerged as a new and powerful technique to investigate the interaction between low-molecular-weight molecules and target proteins. In the present work, the authors assemble from a large compound collection a library of 2226 molecules (fragments having low molecular weights between 100 and 300 Da) to screen them for binding to chymase, a serine protease. Both the active chymase and a zymogen-like form of the protein were used in parallel to distinguish between specific and unspecific binding. The relative ligand-binding activity of the immobilized protein was periodically measured with a reference compound. The screening experiments were performed at 25 degrees C at a fragment concentration of 200 microM in the presence of 2% DMSO. Applying the filter cascade, affinity-selectivity-competition (competition with reference compounds and cross-competition with fragments), 80 compounds show up as positive screening hits. Competition experiments between fragments show that they bind to different parts of the active site. Of 36 fragments co-crystallized for X-ray studies, 12 could be located in the active site of the protein. These results validate the authors' library and demonstrate that the application of SPR technology as a filter in fragment screening can be achieved successfully.
Journal of Biomolecular Screening 05/2009; 14(4):337-49. · 2.05 Impact Factor
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ABSTRACT: Human fructose-1,6-bisphosphatase (FBPase, EC 3.1.3.11) is a key gluconeogenic enzyme, responsible for the hydrolysis of fructose-1,6-bisphosphate to fructose-6-phosphate, and thus presents an opportunity for the development of novel therapeutics focused on lowering the hepatic glucose production in type 2 diabetics. In its active form FBPase exists as a homotetramer and is allosterically regulated by AMP. In an HTS campaign aromatic sulfonylureas have been identified as FBPase inhibitors mimicking AMP. By bridging two adjacent allosteric binding sites using two aromatic sulfonylureas as anchor units and covalently linking them, it was possible to obtain dual binding AMP site inhibitors that exhibit a strong inhibitory effect.
Bioorganic & medicinal chemistry letters 08/2008; 18(16):4708-12. · 2.65 Impact Factor
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Andreas Kuglstatter,
Martin Stahl,
Jens-Uwe Peters, Walter Huber,
Martine Stihle,
Daniel Schlatter,
Jörg Benz,
Armin Ruf,
Doris Roth,
Thilo Enderle,
Michael Hennig
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ABSTRACT: Fragment screening revealed that tyramine binds to the active site of the Alzheimer's disease drug target BACE-1. Hit expansion by selection of compounds from the Roche compound library identified tyramine derivatives with improved binding affinities as monitored by surface plasmon resonance. X-ray structures show that the amine of the tyramine fragment hydrogen-bonds to the catalytic water molecule. Structure-guided ligand design led to the synthesis of further low molecular weight compounds that are starting points for chemical leads.
Bioorganic & medicinal chemistry letters 03/2008; 18(4):1304-7. · 2.65 Impact Factor
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ABSTRACT: The review gives first an introduction into the basics of surface plasmon resonance technology. The physical principle is shortly discussed followed by a discussion of the experimental details to be considered when using this technology for biomolecular interaction analysis. Based on recent publications it is demonstrated that the technology has widespread applications in many fields of the drug discovery process. Protein/protein interactions can be monitored in real time when working with biopharmaceuticals as well as protein/small analyte interactions during hit finding, secondary screening, lead optimization and lead selection. Equilibrium binding constants, kinetic rate constants and thermodynamic parameters are obtained from such study that helps to understand the mechanism of the binding reactions. This information can be directly used to improve binding properties of a drug candidate.
Current pharmaceutical design 02/2006; 12(31):3999-4021. · 4.41 Impact Factor
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ABSTRACT: An immobilization procedure for protein on surface plasmon resonance sensor (SPR) chips is described. The target protein, cyclophilin D, is thereby genetically linked to a mutant of the human DNA repair protein O(6)-alkylguanine-DNA-alkyltransferase (hAGT). The procedure includes the immobilization of an alkylguanine derivative on the surface by amine coupling and contact of the surface with a solution of the fusion protein (TCypD-hAGT). TCypD-hAGT could be immobilized using buffer solutions of purified protein or cell extracts. High densities of covalently linked proteins were achieved by either procedure. Binding experiments performed with the ligand cyclosporin A indicate relative binding activities close to 100%. The K(D) value (12 nM) and the kinetic rate constants k(on) (3 x 10(5)M(-1)s(-1)) and k(off) (4 x 10(-3)s(-1)) are given and compared to values determined for cyclophilin D linked to the surface by amide coupling chemistry. The K(D) value is in excellent agreement with the K(D) value determined in solution by fluorescence titration.
Analytical Biochemistry 11/2004; 333(2):280-8. · 3.00 Impact Factor
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ABSTRACT: Plasma protein binding of drugs has been studied for almost 100 years, but despite the accumulation of large amounts of data, the accurate prediction of this ADME parameter continues to be problematic. This review outlines recent efforts on the development of prediction tools for plasma protein binding of drugs, specifically human serum albumin, in the context of its relevance and its influencing factors. The issue of why it is difficult to achieve prediction of sufficient quality for a diverse dataset will also be considered.
Current opinion in drug discovery & development 08/2004; 7(4):507-12. · 4.20 Impact Factor
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ABSTRACT: Inhibition of dipeptidyl peptidase IV (DPP-IV), the main glucagon-like peptide 1 (GLP1)-degrading enzyme, has been proposed for the treatment of type II diabetes. We expressed and purified the ectodomain of human DPP-IV in Pichia pastoris and determined the X-ray structure at 2.1 A resolution. The enzyme consists of two domains, the catalytic domain, with an alpha/beta hydrolase fold, and a beta propeller domain with an 8-fold repeat of a four-strand beta sheet motif. The beta propeller domain contributes two important functions to the molecule that have not been reported for such structures, an extra beta sheet motif that forms part of the dimerization interface and an additional short helix with a double Glu sequence motif. The Glu motif provides recognition and a binding site for the N terminus of the substrates, as revealed by the complex structure with diprotin A, a substrate with low turnover that is trapped in the tetrahedral intermediate of the reaction in the crystal.
Structure 09/2003; 11(8):947-59. · 6.35 Impact Factor
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ABSTRACT: In spite of the large amount of plasma protein binding data for drugs, it is not obvious and there is no clear consensus among different disciplines how to deal with this parameter in multidimensional lead optimization strategies. In this work, we have made a comprehensive study on the importance of plasma protein binding and the influencing factors in order to get new insights for this molecular property. Our analysis of the distribution of percentage plasma protein binding among therapeutic drugs showed that no general rules for protein binding can be derived, except for the class of chemotherapeutics, where a clear trend towards lower binding could be observed. For the majority of indication areas, however, empirical rules are missing. We present here an extensive list of multiply determined primary association constants for binding to human serum albumin (HSA) for 138 compounds from the literature. Correlating these binding constants with the percentage fraction of protein bound showed that the percentage data above 90%, corresponding to a binding constant below 6 microM, are of insufficient accuracy. Furthermore, it could be demonstrated that the lipophilicity of drugs, traditionally felt to dominate binding to HSA, is not the only relevant descriptor. Here, we report a generic model for the prediction of drug association constants to HSA, which uses a pharmacophoric similarity concept and partial least square analysis (PLS) to construct a quantitative structure-activity relationship. It is able to single out the submicromolar to nanomolar binders, i.e. to differentiate between 99.0 and 99.99% plasma protein binding. Depending on the system, this can be important in medicinal chemistry programs and may together with other computed physicochemical and ADME properties assist in the prioritization of synthetic strategies.
Biochemical Pharmacology 12/2002; 64(9):1355-74. · 4.70 Impact Factor
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Walter Huber
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ABSTRACT: Biophysical label-free assays such as those based on SPR are essential tools in generating high-quality data on affinity, kinetic, mechanistic and thermodynamic aspects of interactions between target proteins and potential drug candidates. Here we show examples of the integration of SPR with bioinformatic approaches and mutation studies in the early drug discovery process. We call this combination 'structure-based biophysical analysis'. Binding sites are identified on target proteins using information that is either extracted from three-dimensional structural analysis (X-ray crystallography or NMR), or derived from a pharmacore model based on known binders. The binding site information is used for in silico screening of a large substance library (e.g. available chemical directory), providing virtual hits. The three-dimensional structure is also used for the design of mutants where the binding site has been impaired. The wild-type target and the impaired mutant are then immobilized on different spots of the sensor chip and the interactions of compounds with the wild-type and mutant are compared in order to identify selective binders for the binding site of the target protein. This method can be used as a cost-effective alternative to high-throughput screening methods in cases when detailed binding site information is available. Here, we present three examples of how this technique can be applied to provide invaluable data during different phases of the drug discovery process.
Journal of Molecular Recognition 18(4):273-81. · 3.31 Impact Factor
