Experimental Therapeutics Programme

Medicinal Chemistry Section

Head of Section:  Sonia Martínez
Research highlights

During 2016, our Section was involved in several projects at different phases of the drug discovery process, among them:

Cyclin-dependent protein kinase 8 inhibitors (CDK8i) project

In this funded project (grant no. SAF2013-44267-R), we have identified lead compound ETP-27, which has served to demonstrate in vivo Proof of Concept (PoC) for CDK8 inhibition in cancer with positive preliminary results. This chemical series was protected by a patent application that reached PCT level in August 2016 and has been exemplified during 2016. Additionally, crystallographic studies with ETP-27 and some analogues from this chemical series have been performed by the CNIO Crystallography and Protein Engineering Unit confirming the expected binding mode of the molecules in the catalytic site.

Currently, we are dedicated to the fine optimisation of the lead compound, trying to increase the oral exposure levels vs time. Modifications in the molecule to reduce Clearance or to increase the Volume of Distribution by introducing basicity, for example, are being considered. The final objective of the project is to obtain an advanced product that is ready for preclinical regulatory development and further clinical studies.


Microtubule-associated serine/threonine protein kinase-like (MASTL) inhibitors

A chemical exploration around the hit identified in the biochemical High-Throughput Screening (HTS) with active full length human MASTL protein has been set up; the aim is to define the pharmacophore required for Mastl activity and to increase the activity of current hits, in order to obtain more potent inhibitors that can be used in biological assays as tool compounds. We will then use this information for the design of novel Mastl inhibitors, including Intellectual Property in their structures.

HASPIN inhibitors

Haspin inhibitors that produce a rapid and efficient mitotic cell death have been identified. We have started a chemical programme in order to explore the current hits and also to generate novel compounds. We are exploring 2 chemical series with haspin inhibitory activity in the low nanomolar range, but also with several main off-targets. Synthesis of analogues has allowed us to learn how selectivity can be achieved without affecting haspin activity. Crystallographic studies of 2 hits from different chemical series have been performed by the CNIO Crystallography and Protein Engineering Unit.

Kinase X* inhibitors

We finalised the Hit-to-Lead phase in collaboration with VIB (Belgium) and have obtained a novel chemical series, in which we identified a potent compound with controlled selectivity and oral bioavailability. The compound has been delivered to VIB to be characterised in different in vivo studies.

Kinase Y* inhibitors

We are collaborating with VIB for the generation of novel inhibitors of a particular kinase. Several reference compounds and analogues have been synthesised in order to help with the validation studies. After analysis of the hits from an HTS campaign, we have concluded that they were not good enough as starting points f plan has been designed and is currently ongoing.

Inhibition of Cancer Stem Cell (CSC) proliferation

In a collaborative project with the CNIO Tumour Suppression Group, we identified several hits that are able to modulate CSC proliferation, stemness and, at sublethal doses, inhibit the tumour initiating capacity of pancreatic CSCs. In order to decipher the target behind the observed phenotype, we have performed chemotype searches linking the structure with potential targets and profiling in broad panels of enzymes and receptors. As a result of the chemical exploration, we have found that the presence of basicity in these molecules is essential for activity. Based on this discovery, we have been able to successfully synthesise different affinity probes by adding a ‘minimalist linker’ to the basic centre, retaining the required cellular activity. These modified molecules, after treatment with cells or cell lysates and photo-irradiation, can covalently capture their binding proteins in a distancedependent manner. The subsequent click chemistry reaction of the terminal alkyne group of the linker with different reporters (i.e. rhodamine-N3 or biotin-N3) enables, via pull-down experiments, the identification of potential cellular protein targets of the drug, as well as imaging-based determination of their cellular localisation. Because these experiments require the use of appropriate controls, we have also been able to synthesise inactive analogues by removing the basicity of the hit and have performed similar pull down and imaging experiments. The already identified candidate targets are going through a validation process.

Telomeric repeat binding factor 1 (TRF1) inhibitors

This project is undertaken in collaboration with the CNIO Telomeres and Telomerase Group. After a screening campaign, using a cell-based assay to measure the removal of TRF1 from telomeres, we have identified several hits, among them ETP946. Our main objective during 2016 has been both the deconvolution of the molecular target behind the observed effect using this hit, as well as the chemical exploration to increase SAR knowledge within this chemical series. In the deconvolution studies, we carried out several chemotype searches and an extensive profiling of the compound against a broad range of enzyme and receptor panels. From these studies we have identified 4 candidate targets that are currently under study. Also, we have generated the first affinity probes by the introduction of appropriate linkers in the molecule that will allow for reversible or irreversible interactions with their molecular targets. Currently, we are testing these probes to address their TRF1 modulation in cells. If they show activity they will be very useful for further imaging localisation and pull-down experiments in order to identify the responsible molecular targets for TRF1 modulation, including TRF1 itself.