Development of Pyridazinone Chemotypes Targeting the PDEδ Prenyl Binding Site

Abstract

The K-Ras GTPase is a major target in anticancer drug discovery. However, direct interference with signaling by K-Ras has not led to clinically useful drugs yet. Correct localization and signaling by farnesylated K-Ras is regulated by the prenyl binding protein PDEδ. Interfering with binding of PDEδ to K-Ras by means of small molecules provides a novel opportunity to suppress oncogenic signaling. Here we describe the identification and structure-guided development of novel K-Ras-PDEδ inhibitor chemotypes based on pyrrolopyridazinones and pyrazolopyridazinones that bind to the farnesyl binding pocket of PDEδ with low nanomolar affinity. We delineate the structure-property relationship and in vivo pharmacokinetic (PK) and toxicokinetic (Tox) studies for pyrazolopyridazinone-based K-Ras-PDEδ inhibitors. These findings may inspire novel drug discovery efforts aimed at the development of drugs targeting oncogenic Ras.

Structure-based development of PDEδ inhibitors

“…This compound retained the potency of Deltazinone 1 (K D = 8 ± 4 nm), while showing a substantial increase in metabolic stability (Table 5). An extended plasma exposure and terminal half-life was found for compound 69 in comparison to Deltazinone 1 (63) after intravenous dosing in mice (Figure 9) (Murarka et al, 2017). These results proved compound 69 to be a valid candidate for further pharmacological development using mouse models.…”

“…This prompted us to develop a novel PDEδ inhibitor chemotype to address the question whether those limitations were chemotype-dependent or intrinsic to the PDEδ-inhibition approach. To identify alternative chemotypes, further analysis of the previously developed high-throughput Alpha Screen hit set pointed towards pyrrolopyridazinone 14 and pyrazolopyridazinone 15 as inhibitors of the PDEδ/KRas interaction (Figure 4) (Papke et al, 2016;Murarka et al, 2017).…”

“…Recently, three different PDEδ-inhibitor chemotypes were developed that bind to the prenyl-binding pocket of PDEδ in vitro with nanomolar affinity (Zimmermann et al, 2014;Murarka et al, 2017). Here we depict the road followed from the hits to the final compounds, guided by X-ray structure determination, modeling studies, biophysical experiments and medicinal chemistry approaches.…”

Diverse chemical and biological potentials of various pyridazine and pyridazinone derivatives

“…The SAR and in vivo pharmacokinetic (PK) and toxicokinetic (Tox) studies for pyrazolopyridazinone-based K-Ras-PDEδ inhibitors. These findings may inspire novel drug discovery efforts aimed at the development of drugs targeting oncogenic Ras (Murarka at al., 2017). Cyclic nucleotide cAMP is a ubiquitous secondary messenger involved in a plethora of cellular responses to biological agents involving activation of adenylyl cyclase.…”

Covalent Protein Labeling at Glutamic Acids

“…Covalent modification of an amino acid in the PDE6d binding site should abrogate inhibitor release. However, the prenyl-binding pocket does not display cysteine or lysine residues available for targeting (Murarka et al, 2016;Zimmermann et al, 2014). Instead, we reasoned that glutamic acid 88 (Glu88), at the upper end of the binding site close to the exit, would be a suitable site for covalent modification by a matching reactive group in the ligand.…”