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The FAIR Cookbook - the essential resource for and by FAIR doers.
No full textThe notion that data should be Findable, Accessible, Interoperable and Reusable, according to the FAIR Principles, has become a global norm for good data stewardship and a prerequisite for reproducibility. Nowadays, FAIR guides data policy actions and professional practices in the public and private sectors. Despite such global endorsements, however, the FAIR Principles are aspirational, remaining elusive at best, and intimidating at worst. To address the lack of practical guidance, and help with capability gaps, we developed the FAIR Cookbook, an open, online resource of hands-on recipes for "FAIR doers" in the Life Sciences. Created by researchers and data managers professionals in academia, (bio)pharmaceutical companies and information service industries, the FAIR Cookbook covers the key steps in a FAIRification journey, the levels and indicators of FAIRness, the maturity model, the technologies, the tools and the standards available, as well as the skills required, and the challenges to achieve and improve data FAIRness. Part of the ELIXIR ecosystem, and recommended by funders, the FAIR Cookbook is open to contributions of new recipes
IAG933, an oral selective YAP1-TAZ/pan-TEAD protein-protein interaction inhibitor (PPIi) with pre-clinical activity in monotherapy and combinations with MAPK inhibitors
No full textThe YAP/TEAD protein-protein interaction is a critical event known to mediate YAP oncogenic functions downstream of the Hippo pathway. All current, advanced pharmacological agents which aim at inhibiting YAP/TEAD oncogenic function do so by engaging into the lipid pocket of TEAD. Thereby the consequences of a direct pharmacological disruption of the interface of YAP and TEADs remain largely unexplored. Here we present IAG933, the first molecule able to potently directly disrupt the YAP/TAZ-TEADs protein-protein interaction with suitable properties to enter in clinical trial.
The path to drug discovery was established by careful and systematic analysis of natural sequences of YAP and TAZ binding to TEAD as well as complemented with structure-based optimization of a truncated natural YAP peptide allowing the pharmacophore mapping of the coil binding site of TEAD. Based on in silico screening, confirmed hit was optimized using structure-based and property-based lead optimization yielding IAG933.
Biochemical and cellular assays demonstrated that IAG933 specifically abrogates the interaction between YAP/TAZ coactivators and all four TEAD isoforms, thus inhibiting TEAD-driven transcriptional activity and inducing cancer cell killing. Exquisite compound selectivity was shown in rescue experiments and is consistent with the correlation observed between pharmacological and genetic sensitivity profiles across a large panel of cancer cell lines.
At the epigenomics level, we observe YAP eviction from chromatin and relocation to the cytoplasm upon treatment with IAG933, leaving TEADs genomic occupancy unaffected and consequently competent to engage its co-repressor VGLL4. Concomitantly, we detect a decrease in enhancer activity and accessibility upon loss of YAP occupancy, which translates to rapid and progressive changes in transcription of Hippo target genes.
In preclinical experiments, IAG933 displays linear pharmacokinetics, consistent with dose proportional in vivo TEAD transcriptional inhibition and anti-tumor efficacy in orthotopic and subcutaneous mouse and rat xenograft and primary-tumor derived malignant pleural mesothelioma models. Importantly, IAG933 elicits complete tumor regression in the MSTO-211H xenograft model at doses that were well tolerated in mice and rats. In line with the current clinical strategy for IAG933, we also demonstrate robust anti-tumor efficacy in cancer models bearing NF2 loss of function or expressing TAZ-fusions.
Moreover, we provide evidence for robust combination benefits of IAG933 with several MAPK/KRAS inhibitors, both in vitro and in vivo, in non-Hippo altered models including lung, pancreatic and colorectal cancer. This is also consistent with IAG933-induced YAP displacement at AP1/TEAD chromatin-binding sites.
Overall, our results provide a robust rationale of progressing IAG933 as monotherapy in patients with Hippo-mutated cancers, and as a combination partner in MAPK-dependent cancers, with the potential to treat several patient populations of high unmet medical need
Design principles for balanced lipophilicity and permeability in beyond Rule of 5 space
No full textA conformational analysis of all oral bRo5 drugs using a QM-based workflow and experimental structures revealed similar polar surface area (PSA) thresholds as for Ro5 drugs and a modest impact of environments on 3D-PSA and intramolecular hydrogen bond (IMHB) count (often termed chameleonicity) despite a significant difference between TPSA and 3D PSA. The minimum TPSA-3D PSA to maintain permeability in bRo5 space depends on the fraction of polarity (TPSA/MW). TPSA/MW in the bRo5 and Ro5 oral drugs sets had a median of ~0.2 Å2/Da, with the upper half corresponding to the upper decile of logP 100 Å2 de-fines the sweet spot of this "rule of 1/5" occupied by the majority of oral bRo5 drugs. TPSA-3DPSA increased in the lead optimization (LO) campaigns of three first in class de novo designed bRo5 drugs and may be a useful parameter for future bRo5 LO campaigns
A conserved metabolic signature associated with response to fast-acting anti-malarial agents
No full textIn malaria drug discovery, understanding the mode of action of lead compounds is important as it helps in predicting the potential emergence of drug resistance in the field when these drugs are eventually deployed. In this study, we have employed metabolomics technologies to characterize the potential targets of anti-malarial drug candidates in the developmental pipeline at NITD. We show that NITD fast-acting leads belonging to spiroindolone and imidazothiadiazole class induce a common biochemical theme in drug-exposed malaria parasites which is similar to another fast-acting, clinically available drug, DHA. These biochemical features which are absent in a slower acting NITD lead (GNF17) point to hemoglobin digestion and inhibition of the pyrimidine pathway as potential action points for these drugs. These biochemical themes can be used to identify and inform on the mode of action of fast drug candidates of similar profiles in future drug discovery programs
In vaccinated individuals serum bactericidal activity against B meningococci is abrogated by C5 inhibition but not by inhibition of the alternative complement pathway
No full textDysregulation of complement activation causes a number of diseases, which can be treated with inhibitors of the complement components C5 and C3. However, complement is required for serum bactericidal activity (SBA) against encapsulated Gram-negative bacteria. Therefore, C3 and C5 inhibition increases the risk of invasive disease, in particular by Neisseria meningitidis. As inhibitors against complement components other than C3 and C5 may carry a reduced risk of infection, we compared the effect of inhibitors targeting the central complement component C3, the alternative pathway (fB and fD), the lectin pathway (MASP-2) and the terminal pathway (C5) on SBA against serogroup B meningococci. Serum from adults was collected before and after vaccination with the meningococcal serogroup B vaccine 4CMenB and tested for meningococcal killing. Since the B capsular polysaccharide is structurally similar to certain human polysaccharides, 4CMenB was designed to elicit antibodies against meningococcal outer membrane proteins. While only a few pre-vaccination sera showed SBA against the B meningococcal isolates tested, 4CMenB vaccination induced potent complement activating IgG titers against isolates expressing a matching allele of the bacterial cell surface-exposed lipoprotein Factor H binding protein (fHbp). While SBA triggered by these cell surface protein-specific antibodies was blocked by C5 and reduced by C3 inhibition, alternative (factor B and D) and lectin (MASP-2) pathway inhibitors had no effect on SBA of post-4CMenB vaccination sera. Compared to SBA triggered by A,C,W,Y capsule polysaccharide conjugate vaccination, SBA against B meningococci expressing a matching fHbp allele, was thus remarkably resilient against alternative pathway inhibition
Two cases of severe pulmonary toxicity from highly active mesothelin-directed CAR T cells.
No full textMultiple clinical studies have treated mesothelin (MSLN)-positive solid tumors by administering MSLN-directed chimeric antigen receptor (CAR) T cells. Although these products are generally safe, efficacy is limited. Therefore, we generated and characterized a potent, fully human anti-MSLN CAR. In a phase 1 dose-escalation study of patients with solid tumors, we observed two cases of severe pulmonary toxicity following intravenous infusion of this product in the high-dose cohort (1-3 × 108 T cells per m2). Both patients demonstrated progressive hypoxemia within 48 h of infusion with clinical and laboratory findings consistent with cytokine release syndrome. One patient ultimately progressed to grade 5 respiratory failure. An autopsy revealed acute lung injury, extensive T cell infiltration, and accumulation of CAR T cells in the lungs. RNA and protein detection techniques confirmed low levels of MSLN expression by benign pulmonary epithelial cells in affected lung and lung samples obtained from other inflammatory or fibrotic conditions, indicating that pulmonary pneumocyte and not pleural expression of mesothelin may lead to dose-limiting toxicity. We suggest patient enrollment criteria and dosing regimens of MSLN-directed therapies consider the possibility of dynamic expression of mesothelin in benign lung with a special concern for patients with underlying inflammatory or fibrotic conditions
Application of clinical and molecular profiling data to improve patient outcomes in psoriatic arthritis.
No full textAchieving a good outcome for a person with Psoriatic Arthritis (PsA) is made difficult by late diagnosis, heterogenous clinical disease expression and in many cases, failure to adequately suppress inflammatory disease features. Single-centre studies have certainly contributed to our understanding of disease pathogenesis, but to adequately address the major areas of unmet need, multi-partner, collaborative research programmes are now required. HIPPOCRATES is a 5-year, Innovative Medicines Initiative (IMI) programme which includes 17 European academic centres experienced in PsA research, 5 pharmaceutical industry partners, 3 small-/medium-sized industry partners and 2 patient-representative organizations. In this review, the ambitious programme of work to be undertaken by HIPPOCRATES is outlined and common approaches and challenges are identified. It is expected that, when completed, the results will ultimately allow for changes in the approaches to diagnosing, managing and treating PsA allowing for better short-term and long-term outcomes
Supported liquid extraction combined with liquid chromatography tandem mass spectrometry for the quantitative analysis of a TLR7 agonist imiquimod LFX453 in plasma at low picogram per milliliter: method validation and its application to pharmacokinetic study in minipig
No full textSample preparation plays a pivotal role in the quantitative determination of low level of compounds in biological fluids by LC-MS/MS. In the present work, we have combined supported liquid extraction (SLE) and LC-MS/MS for the determination of low level a new TLR7 agonist imiquimod, LFX453 under development for the treatment of non-melanoma skin cancer and actinic keratosis. The samples were extracted on ISOLUTE® - SLE 96-well plate by using tert-butyl-methyl ether (MTBE) followed by evaporation and reconstitution of the dry residue with 150 µL of a 0.1% formic acid in acetonitrile/water (50/50, v/v) mixture. Samples were eluted at 0.750 mL/min on Ascentis Express® C18 column (50 mm × 2.1 mm, 2.7 μm) with a mobile phase consisting of 0.1% formic acid in water (A) and 0.1% formic acid in acetonitrile (B). A triple quadrupole mass spectrometer equipped with an electrospray source operating in positive mode was used as detection system. The method run time was 6.5 min and the low limit of quantification (LLOQ) was 1.00 pg/mL with 0.100 mL minipig plasma. Intra-run and inter-run precision and accuracy within the acceptance criteria were achieved during a 3-run validation for quality control samples at four concentration levels over a concentration ranging from 1.00 to 200 pg/mL. The absence of matrix effect demonstrated the usefulness of SLE for the sample preparation. In addition, recovery, 3 freeze thaw cycles and incurred samples reanalysis were validated. The present method was successfully applied to the measurement of LFX453 in plasma after topical application on minipig skin. Our data show that the present method is robust and reliable for the determination of low level of LFX453 in minipig plasma
The role of airway mucus and diseased pulmonary epithelium on the absorption of inhaled antibodies.
No full textInhaled antibody therapy for the treatment of respiratory diseases is a promising strategy to maximize pulmonary exposure and reduce side effects associated with parenteral administration. However, the development of inhaled antibodies is often challenging due to a poor understanding of key mechanisms governing antibody absorption and clearance in healthy and diseased pulmonary epithelium. Here, we utilize well established Human Bronchial Epithelial Cell (HBEC) models grown at air-liquid interface to study the absorption process of antibodies and antibody fragments. With these cellular models, we recapitulate the morphology and function of healthy and diseased pulmonary epithelium, and incorporate the mucosal barrier to enable the investigation of both cellular permeability as well as mucodiffusion. We studied the saturation of antibody transport across the HBEC barriers and estimated the impact of disease-like epithelial barriers on antibody paracellular transport. Additionally, we identified a potential role of neonatal Fc receptor (FcRn)-independent and target-mediated transcytosis in the transport of Fragment antigen-binding (Fab) and F(ab)2 antibody fragments. Lastly, our models were able to pinpoint an impaired antibody diffusion across mucus gels. These mechanistic cellular models are promising in vitro tools to inform Physiologically-based Pharmacokinetic (PBPK) computational models for dose prediction toward de-risking the development of inhaled biologics
Small Angle X-ray Scattering data analysis and theoretical modelling for the size and shape characterization of drug delivery systems based on Vitamin E TPGS micelles
No full textWe developed a simple two-dimensional/two-components theoretical model that describes the structure and functionality of a VitE-TPGS system of micelles assuming a hydrophobic inner core and an outer hydrated hydrophilic shell. We then conceptually applied the developed methodology to a simple system of VitE-TPGS micelles unloaded and loaded with an active pharmaceutical ingredient to verify if the model could reliably monitor the size change of the micelle. The fit of laboratory Small Angle X-Ray Scattering data against such model allows us to extract absolute values of the micelles’ size under a spherical shape hypothesis as well as the distribution within the system between components and level of hydration. The intensity scale of the SAXS experimental data need to be normalized to a reference standard (pure water) to get absolute scattered intensities. The mathematical model which has been developed under a general hypothesis of ellipsoidal micelles, is applied to our experimental data under the simplified spherical assumption, which suitably fit our experimental data