Development of a high-throughput screening platform to identify new therapeutic agents for Medulloblastoma Group 3.

Pediatric brain tumors (PBTs) represent about 25 % of all pediatric cancers and are the most common solid tumors in children and adolescents. Medulloblastoma (MB) is the most frequently occurring malignant PBT, accounting for almost 10 % of all pediatric cancer deaths. MB Group 3 (MB G3) accounts for 25-30 % of all MB cases and has the worst outcome, particularly when associated with MYC amplification. However, no targeted treatments for this group have been developed so far. Here we describe a unique high throughput screening (HTS) platform specifically designed to identify new therapies for MB G3. The platform incorporates optimized and validated 2D and 3D efficacy and toxicity models, that account for tumor heterogenicity, limited efficacy and unacceptable toxicity from the very early stage of drug discovery. The platform has been validated by conducting a pilot HTS campaign with a 1280 lead-like compound library. Results showed 8 active compounds, targeting MB reported targets and several are currently approved or in clinical trials for pediatric patients with PBTs, including MB. Moreover, hits were combined to avoid tumor resistance, identifying 3 synergistic pairs, one of which is currently under clinical study for recurrent MB and other PBTs.

Implementation of mechanism of action biology-driven early drug development for children with cancer.

An urgent need remains for new paediatric oncology drugs to cure children who die from cancer and to reduce drug-related sequelae in survivors. In 2007, the European Paediatric Regulation came into law requiring industry to create paediatric drug (all types of medicinal products) development programmes alongside those for adults. Unfortunately, paediatric drug development is still largely centred on adult conditions and not a mechanism of action (MoA)-based model, even though this would be more logical for childhood tumours as these have much fewer non-synonymous coding mutations than adult malignancies. Recent large-scale sequencing by International Genome Consortium and Paediatric Cancer Genome Project has further shown that the genetic and epigenetic repertoire of driver mutations in specific childhood malignancies differs from more common adult-type malignancies. To bring about much needed change, a Paediatric Platform, ACCELERATE, was proposed in 2013 by the Cancer Drug Development Forum, Innovative Therapies for Children with Cancer, the European Network for Cancer Research in Children and Adolescents and the European Society for Paediatric Oncology. The Platform, comprising multiple stakeholders in paediatric oncology, has three working groups, one with responsibility for promoting and developing high-quality MoA-informed paediatric drug development programmes, including specific measures for adolescents. Key is the establishment of a freely accessible aggregated database of paediatric biological tumour drug targets to be aligned with an aggregated pipeline of drugs. This will enable prioritisation and conduct of early phase clinical paediatric trials to evaluate these drugs against promising therapeutic targets and to generate clinical paediatric efficacy and safety data in an accelerated time frame. Through this work, the Platform seeks to ensure that potentially effective drugs, where the MoA is known and thought to be relevant to paediatric malignancies, are evaluated in early phase clinical trials, and that this approach to generate pre-clinical and clinical data is systematically pursued by academia, sponsors, industry, and regulatory bodies to bring new paediatric oncology drugs to front-line therapy more rapidly.

MMP inhibitors in cardiac diseases: an update.

Close to 60 matrix metalloproteinase (MMP) inhibitors have been pursued as clinical candidates since the first drug discovery program targeting this enzyme family began in the late seventies. Targeted indications included cancer, arthritis, cardiovascular diseases, and many others. However, the clinical development of most of the MMP inhibitors have been discontinued due to safety reasons and so far only Periostat (doxycycline hyclate, a nonspecific MMP inhibitor) has been approved for periodontal disease. Because of the high therapeutic potential, the development of MMP inhibitors continues as shown by several recent patents and scientific publications. Development of selective MMP inhibitors lacking serious side-effects such as musculoskeletal syndrome is of high importance. Innovative approaches for the design of selective MMP inhibitors include the integration of classical medicinal chemistry structure-based properties and design features into the emerging chemogenomics concept of target-family based drug discovery. This approach, which includes privileged structures, molecular frameworks, bioisosteric and bioanalogous/isofunctional modifications (the "matrixinome" approach), may lead to highly selective MMP inhibitors in the future.

Enhanced hit-to-lead process using bioanalogous lead evolution and chemogenomics: application in designing selective matrix metalloprotease inhibitors.

The authors describe an innovative approach for designing novel inhibitors. This approach effectively integrates the emerging chemogenomics concept of target-family-based drug discovery with bioanalogous design strategies, including privileged structures, molecular frameworks as well as bioisosteric and bioanalogous/isofunctional modifications. The authors applied this method in the design of selective inhibitors of matrix metalloproteases (MMPs), also referred to as matrixins, on the basis of a unique analysis of the ligand-target knowledge base, the 'matrixinome'. For this analysis, the authors created an annotated MMP database containing ∼ 300 inhibitors with their published activity profile. The ligand space was then arranged into a lead evolution tree, where the substructural transformations in each virtual step led to marked changes in the activity pattern. This allowed subtype-specific privileged fragments to be extracted as well as modifications, which improve activity and/or selectivity. Furthermore, the compounds with the preferred activity profile were correlated with sequence homology as well as binding site similarity within the target family, thereby leading to the identification of substructural modifications that turn non-selective, biohomologous structures into selective inhibitors. The matrixinomic application of the authors' approach, therefore, provides an example of how the combination of ligand space knowledge with sequence-related data can radically improve the outcome of the lead optimisation process to achieve higher selectivity within a given target family.

Molecular cloning and RNA expression of a novel Drosophila calpain, Calpain C.

The calpains are Ca(2+)-activated cysteine proteases whose biochemical properties have been extensively characterized in vitro. Less is known, however, about the physiological role of calpains. In this respect, Drosophila melanogaster is a useful experimental organism to study calpain activity and regulation in vivo. The sequencing of the fly genome has been recently completed and a novel calpain homologue has been identified in the CG3692 gene product. We embarked on the cloning and characterization of this putative novel calpain. We demonstrate that the actual calpain is different from the predicted protein and we provide experimental evidence for the correction of the genomic annotation. This novel protein, Calpain C, must be catalytically inactive, having mutated active site residues but is otherwise structurally similar to the other known fly calpains. Moreover, we analysed Calpain C RNA expression during Drosophila development by RT-PCR and RNA in situ hybridization, which revealed strong expression in the salivary glands.

A method utilizing differential culture and comparative RT-PCR for determining RNA expression in superior cervical ganglion neurones.

In order to assess the neuronal expression of caspase mRNA in primary cultures of rat superior cervical ganglion (SCG) neurones a method of differential cell purification and comparative RT-PCR was devised. SCG primary cultures generally contain variable percentages of non-neuronal contaminants, which influence RT-PCR results. We optimised a neuronal purification method, allowing the preparation of both highly purified neuronal cultures and mixed cultures, enriched in non-neuronal contaminants. These two sets of cells were cultured in parallel and subsequently analysed by RT-PCR. The use of cell type specific oligonucleotides allowed evaluation of the relative distribution of neuronal (neurofilament) and non-neuronal transcripts in the two cultures. In parallel, specific oligonucleotides were used to detect the mRNA levels of caspase family members. The partition of neurofilament transcript between pure and mixed cultures was found to be statistically different from the partition of the non-neuronal markers. Therefore statistical difference from the partition of non-neuronal markers was taken as evidence for expression in neurones. We show that caspase-2, -3, -6, -7 and -9 transcripts are expressed in SCG neurones whereas caspase-1 is probably absent. Furthermore, none of these transcripts are upregulated during neuronal death induced by nerve growth factor withdrawal. This method could be applied to the analysis of other transcripts in SCG and other primary neuronal cultures containing significant percentages of contaminant cell types.