Design and synthesis of covalent inhibitors and protacs for the protein kinases slk/stk10

Introduction and Justification

Although many successful and historical drugs such as aspirin and penicillin act inhibiting covalently their molecular targets, for a long time the design of drugs with a covalent mechanism of action has been avoided by pharmaceutical industries due to concerns about safety and selectivity. However, pharma-companies and academic researchers have recently revival the design of covalent inhibitors through a rational design, as demonstrated by recent approvals of covalent drugs Sotorasib, a mutant-KRASG12C inhibitor, and Nirmatrelvir, a SARS-CoV2 Mpro inhibitor.
In addition to the classical pharmacology based on occupancy-driven effect, that has enabled us to develop drugs to treat hundreds of diseases, we are now in a new era in Drug Discovery. PROTACs is a new modality of molecular degraders based on a proximity-driven effect. They are heterobifunctional small-molecules constituted by a ligand to bind the protein of interest, a moiety to recruit a E3 ubiquitin ligase, and a linker connecting both parts. This molecule hijacks the ubiquitin-proteasome pathway to induce the degradation of the desired target protein. Currently, the first Protacs are entering in late-stage of clinical trials as well as many others in early-stage pipeline, which demonstrate a promising therapeutic application.
Kinases represent one of the most important human protein families and are directly or indirectly involved in all cellular biochemical pathways. Deregulated kinases have been demonstrated to play a significant role in oncogenesis and aberrant cellular proliferation. Since early 2000’s, 88 kinase inhibitors have entered in the clinics, representing a remarkable success story in drug discovery and development. SLK and STK10 are closely related serine/threonine protein kinases from the Ste20 family and are prime examples of kinases with a strong link to disease but poorly explored by medicinal chemist. Both are involved in the control of the cell cycle and apoptosis and SLK has been associated with overexpression of HER2 receptors in tumors, that latter being a marker of more metastatic and invasive disease with an unfavorable prognosis. Consequently, SLK inhibition may decrease the invasiveness and metastasis in certain types of tumors. SLK/STK10 have been shown to be able to phosphorylate the ezrin/radixin/moesin proteins, and STK10 knockout in vitro demonstrated suppression of prostate cancer cell migration, suggesting an important role of this protein in the tumorigenesis of prostate cancers.
Currently, the most promising SLK/STK10 ligands are reversible inhibitors that have been developed by the applicant and collaborators in previous work (see Serafim et al. J. Med. Chem. 2021, 64, 18, 13259–13278). The most representative molecule showed inhibition of cellular migration in breast carcinoma human cells in a dose-dependent manner. Despite this important result, optimization to improve cellular potency and selectivity is still needed, underlining the potential of these kinases as targets for further endeavors towards obtaining more efficient anti-cancer compounds.

Objectives

Therefore, in order to efficiently target SLK/STK10 via modern mechanisms of action, this project aims to design and synthesize covalent inhibitors and protacs for the protein kinases SLK and STK10. Through molecular modifications of known SLK/STK10 inhibitors used as prototypes, in the covalent strategy we will attach acrylamide as electrophilic group to target a poorly conserved cysteine residue common to both kinases and present in only 21 out of more than 500 other kinases, boosting selectivity and inhibitory activity. In the protacs strategy, we will use a variety of rigid and flexible linkers attached to cereblon-E3 ligase binders, which has been already described to induce STK10 degradation. This study may pave the way for further optimization and subsequent translational drug discovery projects in oncology.

Research Team

The research team is composed by Dr. Serafim (IQS-URL – general coordinator of the project), Dr. Estrada (IQS-URL) and Dr. Elkins (University of Oxford). The three hold complementary synthetic, computational and biological expertise, which is crucial for a successful project in the field of drug discovery. Furthermore, this project will be a kick-off for a strategic scientific IQS-Oxford collaboration, strengthening the partnership between both institutions and improving the IQS-URL internationalization. Lastly, the IQS master students in Pharmaceutical Chemistry (MQF) Enric Brunet, Marc Romo and Xavier Gironella will be actively involved in the synthesis of the compounds as part of their Master’s thesis.