Enabling large-scale design, synthesis and validation of small molecule protein-protein antagonists

Although there is no shortage of potential drug targets, there are only a handful known low-molecular-weight inhibitors of protein-protein interactions (PPIs). One problem is that current efforts are dominated by low-yield high-throughput screening, whose rigid framework is not suitable for the diverse chemotypes present in PPIs. Here, we developed a novel pharmacophore-based interactive screening technology that builds on the role anchor residues, or deeply buried hot spots, have in PPIs, and redesigns these entry points with anchor-biased virtual multicomponent reactions, delivering tens of millions of readily synthesizable novel compounds. Application of this approach to the MDM2/p53 cancer target led to high hit rates, resulting in a large and diverse set of confirmed inhibitors, and co-crystal structures validate the designed compounds. Our unique open-access technology promises to expand chemical space and the exploration of the human interactome by leveraging in-house small-scale assays and user-friendly chemistry to rationally design ligands for PPIs with known structure. © 2012 Koes et al

Fokusierung auf die p53-MDM2 und p53-MDMX Interaktion als therapeutische Strategie für die Antikrebsbehandlung

50 % of all human cancers arise from the deregulation of the wt—p53 pathway, mostly through the activity of the p53 inhibitors MDM2 and MDMX. Hundreds of compounds that disrupt the p53-MDM2 and p53-MDMX interaction were analyzed by FP- and NMR-assays to determine their affinity. X-ray crystallography of the best binding compounds for MDM2 gave insights to the binding mode of these antagonists revealing also a novel 4-point-pharmacophore binding mode. Extensive fluorination scanning of one of the high affinity binding compounds confirms the importance of fluorine in drug research, improving the drug potency. All the results presented in this thesis are of remarkable importance in drug development.50% aller humaner Krebsarten entstehen durch die Deregulation des wt-p53 Stoffwechsels hauptsächlich durch die Aktivität der p53 Inhibitoren MDM2 und MDMX. Hunderte chemischer Verbindungen, die die p53-MDM2 bzw. p53-MDMX Interaktion spalten, wurden mittels FP- und NMR-Methoden analysiert, um deren Affinität zu ermitteln. Röntgenkristallografische Untersuchungen der am besten bindenden chemischen Verbindungen ermöglichten einen Einblick in die Bindungsweise dieser Antagonisten, wodurch auch ein neues „4-point-pharmacophore“ Modell enthüllt wurde. Eine umfassende Fluor-Untersuchung von einer der hoch affinen chemischen Verbindungen bestätigt durch die verbesserte Arzneimittelwirksamkeit die Bedeutung von Fluor in der Arzneimittelforschung. Alle in dieser Arbeit präsentierten Ergebnisse sind von beachtlicher Bedeutung in der Arzneimittelentwicklung

Fragment-based library generation for the discovery of a peptidomimetic p53-Mdm4 inhibitor

On the basis of our recently resolved first cocrystal structure of Mdm4 in complex with a small molecule inhibitor (PDB ID 3LBJ), we devised an approach for the generation of potential Mdm4 selective ligands. We performed the Ugi four-component reaction (Ugi-4CR) in 96-well plates with an indole fragment, which is specially designed to mimic Trp23, a key amino acid for the interaction between p53 and Mdm4. Generally the reaction yielded mostly precipitates collected by 96-well filter plates. The best hit compound was found to be active and selective for Mdm4 (Ki = 5 μM, 10-fold stronger than Mdm2). This initial hit may serve as the starting point for designing selective p53-Mdm4 inhibitor with higher affinity

Konzeption zur beruflichen Fortbildung im Umweltschutz fuer die neuen Bundeslaender

IAB-93-3120-53 AX 464 / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekSIGLEDEGerman

Discovery of highly potent p53-MDM2 antagonists and structural basis for anti-acute myeloid leukemia activities

The inhibition of p53-MDM2 interaction is a promising new approach to non-genotoxic cancer treatment. A potential application for drugs blocking the p53-MDM2 interaction is acute myeloid leukemia (AML) due to the occurrence of wild type p53 (wt p53) in the majority of patients. Although there are very promising preclinical results of several p53-MDM2 antagonists in early development, none of the compounds have yet proven the utility as a next generation anticancer agent. Herein we report the design, synthesis and optimization of YH239-EE (ethyl ester of the free carboxylic acid compound YH239), a potent p53-MDM2 antagoniz ing and apoptosis-inducing agent characterized by a number of leukemia cell lines as well as patient-derived AML blast samples. The structural basis of the interaction between MDM2 (the p53 receptor) and YH239 is elucidated by a co-crystal structure. YH239-EE acts as a prodrug and is the most potent compound that induces apoptosis in AML cells and patient samples. The observed superior activity compared to reference compounds provides the preclinical basis for further investigation and progression of YH239-EE

Representation of the chemical diversity of our multi-component reaction aromatic-biased libraries (different chemotypes shown in different colors) relative to the ZINC database [<b>20</b>] (red dots) and four predicted ligands.

<p>The diversity space is visualized by plotting the top two principal components of the OpenBabel FP2 (<a href="http://openbabel.org" target="_blank">http://openbabel.org</a>) fingerprints of 200,000 compounds randomly selected from the 17.5-and-16 million compounds of ZINC and our aromatic-biased database, respectively. The PPI-biased compounds are focused on a different region of chemical space than the historically-biased ZINC database. Indeed, a library of kinase inhibitors, some containing a tryptophan analog, falls squarely in the space covered by ZINC, while inhibitors of p53/MDM2, including inhibitors without a tryptophan analog, are located in the space covered by the new libraries. Four novel compounds from four distinct scaffolds are found to match anchors on the GP41 dimer <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032839#pone.0032839-Zwick1" target="_blank">[38]</a>, IKK <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032839#pone.0032839-Hacker1" target="_blank">[39]</a>, IL-2 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032839#pone.0032839-Wang1" target="_blank">[40]</a> and EphB2 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032839#pone.0032839-Pasquale1" target="_blank">[41]</a> receptors. Complete reaction chemistries of the <i>AnchorQuery</i> libraries can be found at <a href="http://anchorquery.ccbb.pitt.edu" target="_blank">http://anchorquery.ccbb.pitt.edu</a>.</p

Two crystal structures of p53/MDM2 inhibitors validate the anchor-centric approach and docked models.

<p>In both structures the indole anchor analog of tryptophan overlaps almost perfectly with W23 in p53 (shown in yellow sticks), when the receptors are aligned the MDM2 structure in the co-crystal (PDB 1YCR). (a) The ligand (purple sticks) of PDB 3LBK has a very similar binding mode to the number one hit in our virtual screen (orange sticks). (b) The crystal pose of the <i>AnchorQuery</i> derived compound (purple) with the predicted pose (green) also aligned very well. The presence of a second ligand near the binding interface distorts the receptor shape relative to the receptor used for docking.</p