Reevaluation of bromodomain ligands targeting BAZ2A

BAZ2A promotes migration and invasion in prostate cancer. Two chemical probes, the specific BAZ2-ICR, and the BAZ2/BRD9 cross-reactive GSK2801, interfere with the recognition of acetylated lysines in histones by the bromodomains of BAZ2A and of its BAZ2B paralog. The two chemical probes were tested in prostate cancer cell lines with opposite androgen susceptibility. BAZ2-ICR and GSK2801 showed different cellular efficacies in accordance with their unequal selectivity profiles. Concurrent inhibition of BAZ2 and BRD9 did not reproduce the effects observed with GSK2801, indicating possible off-targets for this chemical probe. On the other hand, the single BAZ2 inhibition by BAZ2-ICR did not phenocopy genetic ablation, demonstrating that bromodomain interference is not sufficient to strongly affect BAZ2A functionality and suggesting a PROTAC-based chemical ablation as an alternative optimization strategy and a possible therapeutic approach. In this context, we also present the crystallographic structures of BAZ2A in complex with the above chemical probes. Binding poses of TP-238 and GSK4027, chemical probes for the bromodomain subfamily I, and two ligands of the CBP/EP300 bromodomains identify additional headgroups for the development of BAZ2A ligands

Combined modification of a TiO2 photocatalyst with two different carbon forms

9 pages, 11 figures, 2 tablesHydrothermally synthesized titanate nanotubes were carbon-doped through a thermal treatment in the presence of glucose followed by blending with single-walled carbon nanotubes (SWCNTs). A series of TiO2-based materials was prepared with various initial glucose contents and two SWCNT types, resulting in total carbon contents from 0.3 wt.% to nearly 26 wt.%. Electron microscopy observations indicated that titanate nanotubes were converted into nanorods during the thermal treatment, and X-ray diffraction patterns confirmed that all the treated materials mostly consisted of anatase TiO2. Glucose pyrolisis caused changes in the infrared and X-ray photoelectron spectra of the titania material, indicating an interaction between the inserted carbon atoms and titanium atoms. Raman spectra of SWCNT/C/TiO2 hybrids showed characteristic bands of both the SWCNT and anatase TiO2 phases. SWCNT/C/TiO2 multicomponent materials demonstrated substantially better photocatalytic activities than P25 TiO2 for methylene blue degradation under visible light irradiation. Independently from its origin, the presence of carbon caused a strong increase in the TiO2 visible light absorption. However, the results obtained with the C/TiO2 and SWCNT/C/TiO2 photocatalysts clearly showed different photocatalysis mechanisms depending on the carbon form.This work was funded by the Government of Aragon and “La Caixa” under project GA-LC-041/2008, the Spanish MINECO under the projects EUI2008-00152, TEC2010-15736, and PRI-PIBAR-2011-1, and the Government of Aragon (DGA) and the European Social Fund (ESF) under Project DGA-ESF-T66 CNN.Peer reviewe

Small Organic Molecules as Tunable Tools for Biology

Drug discovery and development is a very challenging interdisciplinary endeavor that needs the contribution of medical doctors, biologists, chemists, X-ray crystallographers, and computer scientists, among many others, in order to be successful. The first part of this Ph. D. thesis focuses on the development of EphB4 receptor tyrosine kinase inhibitors. EphB4 has been linked to angiogenesis, which involves the formation of new blood vessels supplying tumor cells with the necessary nutrients. Protein kinases play a key role in cell signaling by phosphorylating specific proteins and thus, the inhibition of their enzymatic activity by small organic molecules has been widely explored in drug design. In this work, the biological properties of an EphB4 inhibitor identified by computer simulations were improved by the synthesis of several analogues. Their binding affinities were characterized by an array of biochemical and cell based assays, concluding with the validation of one of the most promising derivatives in an in vivo cancer xenograft model. The second part of the thesis deals with the development of novel bromodomain ligands starting from a micromolar potent in silico discovered hit. Bromodomain proteins are epigenetic readers that constitute an emerging topic in the field of drug discovery and are thus considered as very attractive targets for the development of novel therapeutic drugs. A careful, structure-based design of analogues resulted in the discovery of nanomolar potent CREBBP ligands with an unprecedented selectivity profile among the bromodomain protein family. Moreover, the screening of the synthesized analogues against several cancer cell lines revealed leukemia as a possible therapeutical application for the developed compounds. The third aspect of this work deals with actin: a very attractive, but yet unexplored target in medicinal chemistry. Actin is a cytoskeletal protein that participates in many important cellular functions and has been linked to key pathogenic cellular processes such as angiogenesis, cell adhesion, cytokinesis and metastasis. A new computational approach to discover novel actin leads targeting the ATP binding site of actin resulted in the selection of promising compounds, which were synthesized and tested. The developed small organic molecules constitute valuable tools for the study of actin dynamics as they are able to modify the actin cytoskeleton in cells and moderately inhibit actin polymerization in vitro; thus becoming promising starting hits for the development of more potent actin binders. The last part of this Ph.D. thesis describes the synthesis of neuroprotective compounds by the development of fumaric acid and hydroxytyrosol conjugates, for which the corresponding receptor is unknown. The biological effects of the synthesized analogues are currently under investigation, but the synergistic effect of fumaric acid and hydroxytyrosol is expected to be beneficial in the context of neuroprotection

Discovery of CREBBP bromodomain inhibitors by high-throughput docking and hit optimization guided by molecular dynamics

We have identified two chemotypes of CREBBP bromodomain ligands by fragment-based high-throughput docking. Only 17 molecules from the original library of two-million compounds were tested in vitro. Optimization of the two low-micromolar hits, the 4-acylpyrrole 1 and acylbenzene 9, was driven by molecular dynamics results which suggested improvement of the polar interactions with the Arg1173 side chain at the rim of the binding site. The synthesis of only two derivatives of 1 yielded the 4-acylpyrrole 6 which shows a single-digit micromolar affinity for the CREBBP bromodomain and a ligand efficiency of 0.34 kcal/mol per non-hydrogen atom. Optimization of the acylbenzene hit 9 resulted in a series of derivatives with nanomolar potencies, good ligand efficiency and selectivity (see Unzue, A.; Xu, M.; Dong, J.; Wiedmer, L.; Spiliotopoulos, D.; Caflisch, A.; Nevado, C. Fragment-Based Design of Selective Nanomolar Ligands of the CREBBP Bromodomain. J. Med. Chem. 2015, DOI: 10.1021/acs.jmedchem.5b00172). The in silico predicted binding mode of the acylbenzene derivative 10 was validated by solving the structure of the complex with the CREBBP bromodomain

Fragment-based design of selective nanomolar ligands of the crebbp bromodomain

Novel ligands of the CREBBP bromodomain have been identified by fragment-based docking. The in silico discovered hits have been optimized by chemical synthesis into selective nanomolar compounds thereby preserving the ligand efficiency. The selectivity for the CREBBP bromodomain over other human bromodomain sub-families was achieved by a benzoate moiety which was predicted by docking to be involved in favorable electrostatic interactions with the Arg1173 side chain, a prediction that could be verified a posteriori by the high-resolution crystal structure of the CREBBP bromodomain in complex with ligand 6 and also by MD simulations (see back to back paper)

Structural Analysis of Small-Molecule Binding to the BAZ2A and BAZ2B Bromodomains

The bromodomain-containing protein BAZ2A is a validated target in prostate cancer research, whereas the function of its paralogue BAZ2B is still undefined. The bromodomains of BAZ2A and BAZ2B have a similar binding site for their natural ligand, the acetylated lysine side chain. Here, we present an analysis of the binding modes of eight compounds belonging to three distinct chemical classes. For all compounds, the moiety mimicking the natural ligand engages in essentially identical interactions in the BAZ2A and BAZ2B bromodomains. In contrast, the rest of the molecule is partially solvent-exposed and adopts different orientations with different interactions in the two bromodomains. Some of these differences could be exploited for designing inhibitors with selectivity within the BAZ2 bromodomain subfamily

Back in Person: Frontiers in Medicinal Chemistry 2023

The Frontiers in Medicinal Chemistry (FiMC) is the largest international Medicinal Chemistry conference in the German speaking area and took place from April 3(rd) to 5(th) 2023 in Vienna (Austria). Fortunately, after being cancelled in 2020 and two years (2021-2022) of entirely virtual meetings, due to the COVID-19 pandemic, the FiMC could be held in a face-to-face format again. Organized by the Division of Medicinal Chemistry of the German Chemical Society (GDCh), the Division of Pharmaceutical and Medicinal Chemistry of the German Pharmaceutical Society (DPhG), together with the Division of Medicinal Chemistry of the Austrian Chemical Society (GoCH), the Austrian Pharmaceutical Society (oPhG), and a local organization committee from the University of Vienna headed by Thierry Langer, the meeting brought together 260 participants from 21 countries. The program included 38 lectures by leading scientists from industry and academia as well as early career investigators. Moreover, 102 posters were presented in two highly interactive poster sessions

Binding Motifs in the CBP Bromodomain: An Analysis of 20 Crystal Structures of Complexes with Small Molecules

We analyze 20 crystal structures of complexes between the CBP bromodomain and small-molecule ligands that belong to eight different chemotypes identified by docking. The binding motif of the moiety that mimics the natural ligand (acetylated side chain of lysine) at the bottom of the binding pocket is conserved. In stark contrast, the rest of the ligands form different interactions with different side chains and backbone polar groups on the outer rim of the binding pocket. Hydrogen bonds are direct or water-bridged. van der Waals contacts are optimized by rotations of hydrophobic side chains and a slight inward displacement of the ZA loop. Rare types of interactions are observed for some of the ligands

Understanding the mechanism of action of pyrrolo[3,2-b]quinoxaline-derivatives as kinase inhibitors

The X-ray structure of the catalytic domain of the EphA3 tyrosine kinase in complex with a previously reported type II inhibitor was used to design two novel quinoxaline derivatives, inspired by kinase inhibitors that have reached clinical development. These two new compounds were characterized by an array of cell-based assays and gene expression profiling experiments. A global chemical proteomics approach was used to generate the drug-protein interaction profile, which suggested suitable therapeutic indications. Both inhibitors, studied in the context of angiogenesis and in vivo in a relevant lymphoma model, showed high efficacy in the control of tumor size