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Fevipiprant, a selective prostaglandin-D2 receptor-2 antagonist, inhibits human group-2 innate lymphoid cell aggregation and function
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Optimization of Fused Bicyclic Allosteric SHP2 Inhibitors
No full textSHP2 is a nonreceptor protein tyrosine phosphatase within the mitogen-activated protein kinase (MAPK) pathway controlling cell growth, differentiation, and oncogenic transformation. SHP2 also participates in the programed cell death pathway (PD-1/PD-L1) governing immune surveillance. Small-molecule inhibition of SHP2 has been widely investigated, including in our previous reports describing SHP099 (2), which binds to a tunnel-like allosteric binding site. To broaden our approach to allosteric inhibition of SHP2, we conducted additional hit finding, evaluation, and structure-based scaffold morphing. These studies, reported here in the first of two papers, led to the identification of multiple 5,6-fused bicyclic scaffolds that bind to the same allosteric tunnel as 2. We demonstrate the structural diversity permitted by the tunnel pharmacophore and culminated in the identification of pyrazolopyrimidinones (e.g., SHP389, 1) that modulate MAPK signaling in vivo. These studies also served as the basis for further scaffold morphing and optimization, detailed in the following manuscript
Targeting farnesyl pyrophosphate synthase of Trypanosoma cruzi by fragment-based lead discovery
No full textTrypanosoma cruzi (T. cruzi) is the causative agent of Chagas disease (CD), which mostly affects underprivileged populations in South and Central America. The current standard of care for this disease are the two empirically discovered drugs Benznidazole and Nifurtimox. They show low efficacy, difficulties in administration and severe side effects. Moreover, there are T. cruzi strains that have formed resistances. Thus, the development of a safe and efficient drug is urgently needed. T. cruzi is dependent on isoprenoid biosynthesis as ergosterol and other 24 alkylsterols are essential metabolites that cannot be acquired by other mechanisms. Therefore, it was hypothesised that enzymes along this pathway are promising drug targets. A number of compounds targeting these enzymes were tested and have been shown to inhibit parasite growth. Among those enzymes is farnesyl pyrophosphate synthase (FPPS), a key branch-point enzyme in the isoprenoid pathway, which is in the focus of this work. It catalyses the synthesis of farnesyl pyrophosphate (FPP), a C15 building block in sterol biosynthesis and in protein prenylation of signalling proteins. Bisphosphonates (BPs) are known active site directed FPPS inhibitors, which exhibit ideal pharmacokinetics to target bone mineral and are used to treat bone diseases. BPs can also combat T. cruzi flagellates but are not ideal to treat CD due to their pharmacokinetics. In the search for new chemotypes, several non-BP inhibitors that bind to another pocket were found for human FPPS (hFPPS) by fragment based screening (FBS). Recently, it was shown that the product of FPPS, farnesyl pyrophosphate (FPP), can bind to this pocket and locks the enzyme in an open and inactive state, thus showing the allosteric character of this pocket.
The current work aims at the discovery of non-BP inhibitors of T. cruzi FPPS (TcFPPS), which could be starting points for the development of a treatment against CD. Towards this goal, recombinant expression in E. coli cells and purification by means of IMAC and SEC yielded pure und homogenous TcFPPS (chapter 5.1). This includes unlabelled, 13C15N labelled and in vivo biotinylated avi-tagged TcFPPS. Furthermore, a novel, reliable, highly reproducible, and well-diffracting crystallization system was established. The system exhibits excellent properties for FBS as it was compatible with different types of 96-well plates, including 2 drop and 3 drop SwissCi/MRC, as well as CrystalDirect™ plates. Apo crystals were stable for up to 24 h in 15% DMSO and allowed collection of data sets with a diffraction limit of around 1.6 Å. The highest achieved diffraction limit was 1.28 Å for a soaked TcFPPS crystal (PDB ID 6R09).
The allosteric region in TcFPPS was investigated by means of sequence analysis and structural superimposition of various orthologous FPPSs (chapter 5.2). This revealed that the allosteric region is less conserved than the active site. Differences among residues in equivalent positions that form the allosteric site were observed, which is surprising if it is assumed that all FPPSs can be product inhibited as hFPPS. A remarkable finding is that residue Phe50 in TcFPPS is an exception in an otherwise highly conserved position. It causes steric hindrance of the pocket in TcFPPS. An attempt to reposition established allosteric inhibitors of hFPPS showed binding affinity to TcFPPS but the two obtained crystal structures demonstrated their binding to sites on the protein surface (sites S1 and S2, PDB IDs 6R08 and 6R07, respectively).
The Novartis core and fluorine library (1336 and 482 compounds) were screened on TcFPPS, which resulted in 63 and 45 validated fragment hits, respectively (chapter 5.3). Performing the same screen with T. brucei FPPS (TbFPPS), the causative agent of African sleeping sickness and counter screening on hFPPS led to unique, pairwise and triple binders demonstrating selectivity at the early stage of FBS. Strikingly, TcFPPS has generally more binders than TbFPPS, and TcFPPS has many unique hits when compared to TbFPPS. Subsequent crystallization experiments with the core library hits resulted in 3D structures of two TcFPPS complexes. One ligand binds to the homodimer interface (site S12) and the other one in the active site. The latter was identified by using the statistical analysis tool Pan-Dataset Density Analysis (PanDDA). FBS by X-ray crystallography at the XChem facility in Harwell, UK, and the HTXlab in Grenoble, France, were conducted (chapter 5.4). The XChem screen identified 35 fragment binders (PDB IDs 5QPD – Z, 5QQ0 – 9, 5QQA – C) in binding sites that were distributed over the entire protein. This includes the active site, the allosteric site, the homodimer interface, sites on the surface and a new site in close proximity to the active site. Strikingly, the first two fragments binding to the allosteric site of TcFPPS in its open state were identified. Rotation of the phenyl side chain of Phe50 led to opening of the former closed pocket. The HTXlab screen identified additional binders for the active and allosteric site. In total 1244 data sets were collected and analysed. This process was accelerating using PanDDA.
The first fragment-to-lead optimization by means of virtual screening using the web-based platform ANCHOR.QUERY was based on fragment hit LUY (chapter 5.5). Compounds were synthesised using one-pot one-step multi-component reactions. Synthesis of 11 compounds (MCR 1 – 11) was successful, but poor solubility was detrimental in subsequent testing on TcFPPS and crystallization experiments did not lead to a structure model of a complex. A second fragment to lead optimization using a fragment merging approach for chemical optimization was based on the active site directed binders AWM, LVV, LUY, LDV and AWV (chapter 5.6). A library of 12 compounds (MCN 1 – 12) was synthesised by reductive amination. X-ray structures revealed unexpected binding modes for compounds MCN-1, -4 and -8. Instead of retaining the binding site of the fragment, the merged compounds bind to the surface directed binding site S1 (PDB IDs 6R09, 6R0A, 6R0B). Nevertheless, the 42 crystal structures of TcFPPS-fragment-complexes provided in this work will pave the way for future drug discovery campaigns for CD. The large diversity of the fragments’ scaffolds and different binding sites are potential starting points for inhibitors with different physicochemical properties and a novel mode of action that might help to overcome the limitations related to the BP scaffold
C,N-Disubstituted Biarylpalladacycles as Pre-catalysts for ppm Level Cross Couplings in Water Under Mild Conditions
No full textVarious mono- and di-substitution patterns on the parent biarylamine skeleton characteristic of palladacycles, as well as the counterion effect, have been studied looking to increase the binding constant of the resulting palladacycle to the inner cores of nanomicelles in water, thereby reducing the amount of Pd needed for coupling reactions. Several substituted palladacycles containing readily accessible ligands were chosen for evaluation. The results indicate that: (1) pre-activation of
these pre-catalysts for Suzuki-Miyaura (SM) couplings can be avoided; (2) reactions could be performed with ca. half the loading of Pd as previously required for use of (Pd salts + ligand)
combinations; (3) the most effective palladacycle has been identified as that containing an isopropyl
group on both an aryl ring and on nitrogen, together with ligand EvanPhos and triflate as the counterion (P12). This pre-catalyst is also effective in other C-C bond forming reactions, such as Heck and Sonogashira couplings. No organic solvents were needed for these processes, while the aqueous reaction medium could be recycled several times. A 1–pot, 4–step sequence involving Suzuki-Miyaura, reduction, alkylation, and acylation reactions highlights the potential for this pre-catalyst to maximize synthetic gain while minimizing costs and waste generation
Assessment of Mouse Handling Techniques During Cage Changing.
No full textMouse handling during cage changing and health evaluation has traditionally been performed by using forceps. This method was adopted as a biosecurity measure but can adversely affect employee ergonomics and rodent behavior. In this study, we evaluated alternative methods of rodent handling and their potential implications for efficiency, biosecurity, and animal welfare. Study groups included plastic cups, gloved hands, 2 methods of tunnel handling, and forceps. Evaluations included speed of cage change, ATP-based assessment of sanitization, and retrospective analysis of colony health and breeding data. The time to change 14 cages was significantly faster at each time point for the gloved hands and forceps groups as compared with the other methods. Overall speed did not increase significantly with each subsequent study week for anygroup. ATP levels after sanitization with hydrogen peroxide-peracetic acid mixture differed significantly between gloves and forceps. When ATP level was evaluated on a per-cm2 basis, no significant difference between gloves and forceps was detected. Although tunnel and cup handling both increased the time for cage-changing, the tunnel served as both an indirect handling method and a shelter when left within the cage. Retrospective analysis revealed that breeding performance and colony health were similar among groups. Although efficiency is a concern for large-scale implementation of novel handling methods, the tunnel method may prove beneficial for sensitive strains or studies requiring indirect handling. In addition, using gloved hands to directly handle mice during cage changing is efficient and avoids the ergonomic strain associated with forceps. Precautions should be taken when handling mice with gloves, given that the increased contact area carries an increased load of organic debris. Changing gloves between rack sides or before proceeding to the animals belonging to a different investigator minimizes the potential for cross-contamination
Structure-based and property-driven optimization of N-aryl imidazoles towards potent and selective oral RORγt inhibitors
No full textRORγt is considered the master transcription factor for the development of Th17 cells that produce pro-inflammatory cytokines such as IL-17A. Overproportionate Th17 cell abundance is associated with the pathogenesis of many inflammatory conditions including psoriasis. In a high-throughput FRET screen, we identified compound 1 as hit with promising lipE. Using structure-based drug design based on a number of X-ray co-crystal structures, we morphed this hit class into potent imidazoles, exemplified by compound 3. To improve the poor ADME properties of neutral imidazoles, we extended our ligands with carboxylic acid substituents towards a polar, water rich area of the protein. This highly lipophilicity efficient modification ultimately led to the discovery of compound 14, a potent and selective inhibitor of RORγt with good ADME properties and excellent in vivo pharmacokinetics. This compound showed good efficacy in an in vivo delayed-type hypersensitivity pharmacology model in rats
Prediction of pKa Using Machine Learning Methods with Rooted Topological Torsion Fingerprints: Application to Aliphatic Amines.
No full textThe acid-base dissociation constant, p, is a key parameter to define the ionization state of a compound and directly affects its biopharmaceutical profile. In this study, we developed a novel approach for p prediction using rooted topological torsion fingerprints in combination with five machine learning (ML) methods: random forest, partial least squares, extreme gradient boosting, lasso regression, and support vector regression. With a large and diverse set of 14 499 experimental p values, p models were developed for aliphatic amines. The models demonstrated consistently good prediction statistics and were able to generate accurate prospective predictions as validated with an external test set of 726 p values (RMSE 0.45, MAE 0.33, and 0.84 by the top model). The factors that may affect prediction accuracy and model applicability were carefully assessed. The results demonstrated that rooted topological torsion fingerprints coupled with ML methods provide a promising approach for developing accurate p prediction models
Auxin-inducible depletion of the essentialome suggests inhibition of TORC1 by auxins and inhibition of Vrg4 by SDZ 90-215, a natural antifungal cyclopeptide
No full textGene knockout and knockdown strategies have been immensely successful probes of gene function, but small molecule inhibitors (SMIs) of gene products allow much greater time resolution and are particularly useful when the targets are essential for cell replication or survival. SMIs also serve as lead compounds for drug discovery. However, discovery of selective SMIs is costly and inefficient. The action of SMIs can be modeled simply by tagging gene products with an auxin-inducible degron (AID) that triggers rapid ubiquitylation and proteasomal degradation of the tagged protein upon exposure of live cells to auxin. To determine if this approach is broadly effective, we AID-tagged over 750 essential proteins in Saccharomyces cerevisiae and observed growth inhibition by low concentrations of auxin in over 66% of cases. Polytopic transmembrane proteins in the plasma membrane, Golgi complex, and endoplasmic reticulum were efficiently depleted if the AID-tag was exposed to cytoplasmic OsTIR1 ubiquitin ligase. The auxin analog 1-napthylacetic acid (NAA) was as potent as auxin on AID-tags, but surprisingly NAA was more potent than auxin at inhibiting target of rapamycin complex 1 (TORC1) function. Auxin also synergized with known SMIs when acting on the same essential protein, indicating that AID-tagged strains can be useful for SMI screening. Auxin synergy, resistance mutations, and cellular assays together suggest the essential GMP/GDP-mannose exchanger in the Golgi complex (Vrg4) as the target of a natural cyclic peptide of unknown function (SDZ 90-215). These findings indicate that AID-tagging can efficiently model the action of SMIs before they are discovered and can facilitate SMI discovery
Implementation and Relevance of FAIR Data Principles in Biopharmaceutical Research and Development
No full textBiopharmaceutical industry R&D, and indeed other Life Sciences R&D such as agri-food, is data-driven and can significantly improve its efficiency and effectiveness by implementing the FAIR (Findable, Accessible, Interoperable, Reusable) Guiding Principles for scientific data management and stewardship. By so doing, the plethora of new and powerful analytical tools such as artificial intelligence and machine learning will be able automatically and at scale to access the data from which they learn, and on which they thrive. FAIR is a fundamental enabler for digital transformation
YAP, but Not RSPO-LGR4/5, Signaling in Biliary Epithelial Cells Promotes a Ductular Reaction in Response to Liver Injury.
No full textBiliary epithelial cells (BECs) form bile ducts in the liver and are facultative liver stem cells that establish a ductular reaction (DR) to support liver regeneration following injury. Liver damage induces periportal LGR5+ putative liver stem cells that can form BEC-like organoids, suggesting that RSPO-LGR4/5-mediated WNT/β-catenin activity is important for a DR. We addressed the roles of this and other signaling pathways in a DR by performing a focused CRISPR-based loss-of-function screen in BEC-like organoids, followed by in vivo validation and single-cell RNA sequencing. We found that BECs lack and do not require LGR4/5-mediated WNT/β-catenin signaling during a DR, whereas YAP and mTORC1 signaling are required for this process. Upregulation of AXIN2 and LGR5 is required in hepatocytes to enable their regenerative capacity in response to injury. Together, these data highlight heterogeneity within the BEC pool, delineate signaling pathways involved in a DR, and clarify the identity and roles of injury-induced periportal LGR5+ cells