Experimental Therapeutics Programme

Medicinal Chemistry Section

Head of Section:  Sonia Martínez
Research highlights

Project advances in 2017:

Cyclin-dependent protein kinase 8 inhibitors (CDK8i) project

During 2017, we were involved in the optimisation of ETP-27; a lead compound identified and developed in our programme, with demonstrated in vivo proof-of-concept in the acute myeloid leukaemia model, MOLM-13 xenograft. Fine tuning optimisation has been done and we have identified ETP-93, an orally bioavailable compound with longer half-life than ETP-27. ETP-93 showed oral levels in both plasma and tumour, biomarker modulation (pSTAT1) up to 8 hours after oral administration in PK/PD studies, and a significant tumour growth inhibition of 50% in a 10 day short-term study at 50 mpk P.O. in MOLM-13. The compound is rather selective (S(35): 0.08) in a 468 kinase panel (KINOMEscanTM platform) and only 1 main off-target has been identified. Currently, we are evaluating the positive contribution of this activity to the antiproliferative profile of the compound. Additionally, in this series we have identified very selective CDK8 inhibitors with good in vivo PK, for example ETP-18, which has been selected for further in vivo efficacy studies.

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

Two different hits were identified from an HTS campaign with active full length human MASTL protein. About 100 analogues have been synthesised around them to establish StructureActivity-Relationships (SAR), identifying compounds in the single digit nanomolar range from both chemical series. Selected compounds have been profiled in a small set of kinases to determine their selectivity and we have identified some main off-targets in the compounds. Currently, we are focussing our efforts on trying to obtain high quality selective chemical probes that will be used in pharmacological inhibition studies to decipher the whole therapeutic potential of MASTL.

HASPIN inhibitors

During the exploration of 2 chemical series we were able to obtain very potent biochemical and cellular low nanomolar haspin inhibitors, while removing the off-target activities present in the original hits. After the synthesis of about 90 compounds, we profiled the selectivity of 2 representative molecules from each chemical series, ETP-949 and ETP-885, in a 468 kinase panel (KINOMEscanTM) obtaining a high level of selectivity for both of them (S(35) of 0.025 and 0.007). Currently, one of these chemical series is under in vivo characterisation with the aim of identifying a high quality Haspin inhibitor for pharmacological target validation studies. Additionally, a third chemical series was generated in 2017, including intellectual property in the design.

Inhibition of Cancer Stem Cell (CSC) proliferation

This project is undertaken in collaboration with the CNIO Tumour Suppression Group. After the identification of compounds able to modulate CSC proliferation, stemness and, at sublethal doses, inhibit the tumour initiating capacity of pancreatic CSCs, we generated affinity probes by introducing a minimalist linker, retaining the activity; these probes were used in deconvolution studies in 2017. The presence of the minimalist linker increased the efficiency of these studies by enabling the formation of a covalent linkage with the binding proteins after photo-irradiation treatment. Additionally, we have scaled up the hit compound to evaluate its in vivo pharmacokinetic properties.

Telomeric repeat binding factor 1 (TRF1) inhibitors

This is a collaborative project undertaken with the CNIO Telomeres and Telomerase Group. During 2017, we focused on the synthesis of different affinity probes of hit compound ETP-946 in order to identify the putative molecular target responsible for the observed TRF1 modulation. Among them, the ETP-455 affinity probe showed similar TRF1 modulation to the hit compound and was selected for deconvolution studies. ETP-455 contains a reversible linker with a terminal alkyne reactive group that helps in cell localisation and pull down experiments by using a click chemistry reaction with functionalised (azide reactive group) fluorophores and/or biotinylated derivatives. Preliminary cell localisation experiments using imaging techniques have been performed, demonstrating a rather specific localisation of the chemical probe that can be removed by competition with ETP-946.