Synthesis of fatty acid mimetics and their characterization as PPARalpha/gamma agonists and dual mPGES-1/5-LO inhibitors

Die vorliegende, in kumulativer Schreibweise verfasste Arbeit erläutert die Entwicklung, Charakterisierung und Optimierung zweier unter­schiedlicher Leit­strukturen, die als Agonisten von Peroxisomen Proliferator-aktivierten Rezeptoren (PPAR) und gleichsam als duale Inhibitoren der mikrosomalen Prostaglandin E2 Synthase-1 (mPGES-1) und der 5-Lipoxygenase (5-LO) wirken. Chemisch betrachtet sind dies zum ersten die Gruppe der alpha-n-Hexyl-Pirinixin­säurederivate und zum zweiten die Gruppe der 2-(Phenylthio)-hexan­säurederivate. Die Publikation zur Synthese und in vitro-pharmakologischen Charakterisierung der alpha-n-Hexyl-Pirinixinsäurederivate an PPAR (Zettl et al., QSAR & Combinatorial Science, 28:576–586, 2009) enthält einerseits die strukturelle Optimierung durch Variation der Aryl-Substitution des zentralen Pyrimidinringes der Leitstruktur und andererseits die durch Docking-Verfahren gestützte Untersuchung des Einflusses der Stereochemie auf die PPAR-Aktivierung. Letztlich konnte durch die Einführung von Biphenyl-Substituenten eine Verbesserung insbesondere der PPARalpha-Aktivität gegenüber der als strukturellen Referenz dienenden alpha-n-Hexyl-Pirinixinsäure (Rau et al., Archiv der Pharmazie, 341:191–195, 2008) erreicht werden. Mit Hilfe von präparativer enantioselektiver HPLC wurde eine ausgewählte Verbindung in ihre beiden Enantiomere getrennt. Deren in vitro-pharmakologische Charakterisierung ergab, dass das (R)-Enantiomer insbesondere bei PPARalpha als Eutomer fungiert. Dieses Ergebnis konnte mit Hilfe von Docking-Studien weiter untermauert werden. Hierbei wurde deutlich, dass die Besetzung der linken proximalen Bindetasche der PPARalpha-Liganden-Bindungs-Domäne durch den alpha-n-Hexyl-Rest lediglich im Fall einer (R)-Konfiguration optimal erfolgen kann. Die Synthese und die in vitro-pharmakologische Charakterisierung der Substanz­klasse der 2-(Phenylthio)-hexansäurederivate an PPAR sind in Zettl et al., Bioorganic & Medicinal Chemistry Letters, 19: 4421-4426, 2009 zusammengefasst. Bei der Analyse der Struktur-Wirkungs-Beziehungen erwies sich die Leitstruktur als hochaktiv und sehr robust. Je nach Substitutionsmuster des lipophilen Molekülteils wurden potente selektive PPARalpha-Agonisten wie auch PPARalpha-präferenzielle duale PPARalpha/gamma-Agonisten dargestellt. Durch die Synthese von Kohlenstoff-Analoga und alpha-unsubsti­tuierten Verbindungen wurde des Weiteren der Einfluss des Schwefelatoms und des n-Butylrestes in alpha-Position zur Carbonsäure auf die PPAR-Aktivität untersucht. Hierbei konnte gezeigt werden, dass beide Strukturelemente einen großen Beitrag zur hohen PPARalpha-Aktivität der Leitstruktur leisten. Wie auch bei den alpha-n-Hexyl-Pirinixinsäurederivaten wurde eine ausgewählte Verbindung in ihre Enantiomere getrennt und der Einfluss des Stereozentrums in alpha-Position zur Carbon­säure untersucht. Das Ergebnis bestätigte die Resultate der vorangegangenen Studie: Das (R)-Enantiomer wirkte als Eutomer, wobei der stereochemische Einfluss bei PPARalpha besonders deutlich war. Ausgewählte Synthesen und die in vitro-pharmakologische Charakterisierung von Pirinixinsäurederivaten an mPGES-1, 5-LO sowie der Cyclooxygenase (COX) sind in Koeberle und Zettl et al., Journal of Medicinal Chemistry, 51:8068–8076, 2009 publiziert. Die Arbeit beinhaltet eine umfassende Reihe an Pirinixinsäurederivaten mit Strukturvariationen in alpha-Position zur Carbonsäure und im Aryl-Substitutions­muster des Pyrimidinringes. Hinsichtlich der alpha-Substitution zeigte sich, dass für Alkylreste eine Kettenlänge von mindestens 6 Kohlenstoffatomen für einen dualen Wirkmechanismus erforderlich ist. Als Leitstruktur für duale mPGES-1/5-LO-Inhibitoren ergab sich somit alpha-n-Hexyl-substituierte Pirinixin­säure, deren Aryl-Substitutionsmuster am zentralen Pyrimidin weiter optimiert wurde. Als vorteilhaft erwies sich die Substitution mit Biphenylresten, wodurch die Darstellung von niedrig mikromolar aktiven dualen mPGES-1/5-LO-Inhibitoren gelang. Bei der Analyse der Strukur-Wirkungs-Beziehungen von unterschiedlichen Biphenylresten zeigte sich eine hohe strukturelle Toleranz hinsichtlich der dualen inhibitorischen Aktivität an der mPGES-1 und der 5-LO. Somit stellen die alpha-n-Hexyl-Pirinixin­säurederivate die ersten publizierten dualen mPGES-1/5-LO-Inhibitoren dar.This cumulative thesis summarizes and discusses the content of the followed articles: 1. Novel Pirinixic Acids as PPARalpha Preferential Dual PPARalpha/gamma Agonists Zettl H, Dittrich M, Steri R, Proschak E, Rau O, Steinhilber D, Schneider G, Lämmerhofer M, Schubert-Zsilavecz M QSAR & Combinatorial Science 2009; 28, 576-586. Abstract: Pirinixic acid is a moderate agonist of both the alpha and the gamma subtype of the peroxisome proliferator activated receptor (PPAR). Previously, we have shown that alpha-alkyl substitution leads to balanced low micromolar-active dual agonists of PPARalpha and PPARgamma. Taking alpha-hexyl pirinixic acid as a new scaffold, we further optimized PPAR activity by enlargement of the lipophilic backbone by substituting the 2,3-dimethylphenyl with biphenylic moieties. Such a substitution pattern had only minor impact on PPARgamma activity but further increased PPARalpha activity leading to nanomolar activities. Supporting docking studies proposed that the (R)-enantiomer should fit the PPARalpha ligand-binding pocket better and thus be more active than the (S)-enantiomer. Single enantiomers of selected active analogues were then prepared by enantio-selective synthesis and enantio-selective preparative HPLC, respectively. Biological data for the distinct enantiomers fully corroborated the docking experiments and substantiate a stereochemical impact on PPAR activation. 2. Discovery of a novel class of 2-mercaptohexanoic acid derivatives as highly active PPARalpha agonists Zettl H, Steri R, Lämmerhofer M, Schubert-Zsilavecz M Bioorg Med Chem Lett 2009; 19, 4421-4426. Abstract: A novel and robust scaffold for highly active PPARalpha agonists based on the 2-mercaptohexanoic acid substructure is presented. Systematic structural variation of the substitution pattern of the phenolic backbone yielded detailed SAR especially of ortho and meta substituents. We corroborated the importance of the sulfur atom as well as of the n-butyl chain for PPARalpha activity in the 2-mercaptohexanoic acid head group by preparation of carbon analogs and alpha-unsubstituted derivatives. Compound 10 represents a low nano molar active PPARalpha activator with excellent selectivity towards PPARgamma. 3. Pirinixic Acid Derivatives as Novel Dual Inhibitors of Microsomal Prostaglandin E2 Synthase-1 and 5-Lipoxygenase Koeberle A, Zettl H, Greiner C, Wurglics M, Schubert-Zsilavecz M, Werz O J Med Chem 2008; 51, 8068-8076. Abstract: Dual inhibition of the prostaglandin (PG) and leukotriene (LT) biosynthetic pathway is supposed to be superior over single interference, both in terms of efficacy and side effects. Here, we present a novel class of dual microsomal PGE2 synthase-1/5-lipoxygenase (5-LO) inhibitors based on the structure of pirinixic acid [PA, 2-(4-chloro-6-(2,3-dimethylphenylamino)pyrimidin-2-ylthio)acetic acid, compound 1]. Target-oriented structural modification of 1, particularly alpha-substitution with extended n-alkyl or bulky aryl substituents and concomitant replacement of the 2,3-dimethylaniline by a biphenyl-4-yl-methane-amino residue, resulted in potent suppression of mPGES-1 and 5-LO activity, exemplified by 2-(4-(biphenyl-4-ylmethylamino)-6-chloropyrimidin-2-ylthio)octanoic acid (7b, IC50 ) 1.3 and 1 microM, respectively). Select compounds also potently reduced PGE2 and 5-LO product formation in intact cells. Importantly, inhibition of cyclooxygenases-1/2 was significantly less pronounced. Taken together, these pirinixic acid derivatives constitute a novel class of dual mPGES-1/5-LO inhibitors with a promising pharmacologial profile and a potential for therapeutic use

SQUIRRELnovo : de novo design of a PPARalpha agonist by bioisosteric replacement

Shape complementarity is a compulsory condition for molecular recognition. In our 3D ligand-based virtual screening approach called SQUIRREL, we combine shape-based rigid body alignment with fuzzy pharmacophore scoring. Retrospective validation studies demonstrate the superiority of methods which combine both shape and pharmacophore information on the family of peroxisome proliferator-activated receptors (PPARs). We demonstrate the real-life applicability of SQUIRREL by a prospective virtual screening study, where a potent PPARalpha agonist with an EC50 of 44 nM and 100-fold selectivity against PPARgamma has been identified..

Kernel learning for ligand-based virtual screening: discovery of a new PPARgamma agonist

Poster presentation at 5th German Conference on Cheminformatics: 23. CIC-Workshop Goslar, Germany. 8-10 November 2009 We demonstrate the theoretical and practical application of modern kernel-based machine learning methods to ligand-based virtual screening by successful prospective screening for novel agonists of the peroxisome proliferator-activated receptor gamma (PPARgamma) [1]. PPARgamma is a nuclear receptor involved in lipid and glucose metabolism, and related to type-2 diabetes and dyslipidemia. Applied methods included a graph kernel designed for molecular similarity analysis [2], kernel principle component analysis [3], multiple kernel learning [4], and, Gaussian process regression [5]. In the machine learning approach to ligand-based virtual screening, one uses the similarity principle [6] to identify potentially active compounds based on their similarity to known reference ligands. Kernel-based machine learning [7] uses the "kernel trick", a systematic approach to the derivation of non-linear versions of linear algorithms like separating hyperplanes and regression. Prerequisites for kernel learning are similarity measures with the mathematical property of positive semidefiniteness (kernels). The iterative similarity optimal assignment graph kernel (ISOAK) [2] is defined directly on the annotated structure graph, and was designed specifically for the comparison of small molecules. In our virtual screening study, its use improved results, e.g., in principle component analysis-based visualization and Gaussian process regression. Following a thorough retrospective validation using a data set of 176 published PPARgamma agonists [8], we screened a vendor library for novel agonists. Subsequent testing of 15 compounds in a cell-based transactivation assay [9] yielded four active compounds. The most interesting hit, a natural product derivative with cyclobutane scaffold, is a full selective PPARgamma agonist (EC50 = 10 ± 0.2 microM, inactive on PPARalpha and PPARbeta/delta at 10 microM). We demonstrate how the interplay of several modern kernel-based machine learning approaches can successfully improve ligand-based virtual screening results

Flexible, Heat-Resistant, and Flame-Retardant Glass Fiber Nonwoven/Glass Platelet Composite Separator for Lithium-Ion Batteries

A new type of high-temperature stable and self-supporting composite separator for lithium-ion batteries was developed consisting of custom-made ultrathin micrometer-sized glass platelets embedded in a glass fiber nonwoven together with a water-based sodium alginate binder. The physical and electrochemical properties were investigated and compared to commercial polymer-based separators. Full-cell configuration cycling tests at different current rates were performed using graphite and lithium iron phosphate as electrode materials. The glass separator was high-temperature tested and showed a stability up to at least 600 °C without significant shrinking. Furthermore, it showed an exceptional wettability for non-aqueous electrolytes. The electrochemical performance was excellent compared to commercially available polymer-based separators. The results clearly show that glass platelets integrated into a glass fiber nonwoven performs remarkably well as a separator material in lithium-ion batteries and show high-temperature stability

DOGS: Reaction-Driven de novo Design of Bioactive Compounds

We present a computational method for the reaction-based de novo design of drug-like molecules. The software DOGS (Design of Genuine Structures) features a ligand-based strategy for automated ‘in silico’ assembly of potentially novel bioactive compounds. The quality of the designed compounds is assessed by a graph kernel method measuring their similarity to known bioactive reference ligands in terms of structural and pharmacophoric features. We implemented a deterministic compound construction procedure that explicitly considers compound synthesizability, based on a compilation of 25'144 readily available synthetic building blocks and 58 established reaction principles. This enables the software to suggest a synthesis route for each designed compound. Two prospective case studies are presented together with details on the algorithm and its implementation. De novo designed ligand candidates for the human histamine H4 receptor and γ-secretase were synthesized as suggested by the software. The computational approach proved to be suitable for scaffold-hopping from known ligands to novel chemotypes, and for generating bioactive molecules with drug-like properties

Comparative thermodynamic analysis of dna-protein interactions using surface plasmon resonance and fluorescence correlation spectroscopy

We report a kinetic and thermodynamic analysis of interactions between ssDNA and replication protein A (RPA) using surface plasmon resonance (SPR) and fluorescence correlation spectroscopy (FCS) at variable temperature. The two methods yield different values for the Gibbs free energy but nearly the same value for the reaction enthalpy of ssDNA-RPA complex formation. The Gibbs free energy was determined by SPR and FCS to be -62.6 and -54.7 kJ/mol, respectively. The values for the reaction enthalpy are -64.4 and -66.5 kJ/mol. It is concluded that the difference in Gibbs free energy measured by the two methods is due to different reaction entropies. The entropic contribution to the free energy at 25 degreesC is -1.8 kJ/mol for SPR and -11.8 kJ/mol for FCS. In SPR, the reaction is restricted to two dimensions because of immobilization of the DNA molecules to the sensor surface. In contrast, FCS is able to follow complex formation without spatial restrictions. In consequence, the reaction entropy determined from SPR experiments is lower than for FCS experiments

Micellar Aggregates of Amylose-block-polystyrene Rod-Coil Block Copolymers in Water and THF

Amylose-block-polystyrenes with various block copolymer compositions were investigated in water and in THF solution. Fluorescence correlation spectroscopy, dynamic light scattering (DLS), and asymmetric flow field-flow fractionation with multiangle light scattering detection indicate the presence of unimers, oligomers, and large micellar species in THF. Up to four different species were detectable by DLS with hydrodynamic radii ranging from a few nanometers to >10 µm, indicating that the system is not in a thermodynamic equilibrium state. Collapsed aggregates were monitored on a silicon surface by scanning force microscopy and transmission electron microscopy. In water, crew-cut micelles were obtained from the same block copolymers by a single solvent approach, using elevated temperature and pressure. These crew-cut aggregates are much more uniform than the respective star aggregates in THF, and their radii scale with Rh ∝ Ncore^1/4, Rh ∝ Ncorona^1/6 in solution and with R ∝ Ncore^1/4, R ∝ Ncorona^1/2 on a silicon surface.