Structure–Activity Relationship (SAR) Study of Spautin-1 to Entail the Discovery of Novel NEK4 Inhibitors

Abstract

Lung cancer is one of the most frequently diagnosed cancers accounting for the highest number of cancer-related deaths in the world. Despite significant progress including targeted therapies and immunotherapy, the treatment of advanced lung cancer remains challenging. Targeted therapies are highly efficacious at prolonging life, but not curative. In prior work we have identified Ubiquitin Specific Protease 13 (USP13) as a potential target to significantly enhance the efficacy of mutant EGFR inhibition. The current study aimed to develop lead molecules for the treatment of epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancer (NSCLC) by developing potent USP13 inhibitors initially starting from Spautin-1, the only available USP13 inhibitor. A SAR study was performed which revealed that increasing the chain length between the secondary amine and phenyl group and introducing a halogen capable of inducing a halogen bond at position 4’ of the phenyl group, dramatically increased the activity. However, we could not confirm the binding between Spautin-1 (or its analogues) and USP13 using isothermal titration calorimetry (ITC) or thermal shift assay (TSA) but do not exclude binding under physiological conditions. Nevertheless, we found that the anti-proliferative activity displayed by Spautin-1 towards EGFR-mutant NSCLC cells in vitro was at least partially associated with kinase inhibition. In this work, we present N-[2-(substituted-phenyl)ethyl]-6-fluoro-4-quinazolinamines as promising lead compounds for the treatment of NSCLC. These analogues are significantly more effective towards EGFR-mutant NSCLC cells than Spautin-1 and act as potent never in mitosis A related kinase 4 (NEK4) inhibitors (IC50~1 µM) with moderate selectivity over other kinases.

A Protein-Ligand Interaction-focused 3D Molecular Generative Framework for Generalizable Structure-based Drug Design

“…A leucine-toarginine mutation at residue 858(L858R) in a kinase domain of EGFR is one of the most frequently observed causes of non-small-cell lung cancer. [31,52] Despite the early trials that have developed drugs to target the single-site mutated EGFR, patients often exhibit drug resistance due to the gate-keeper mutation of T790M. [53][54][55] Thus, developing a drug to selectively inhibit an L858R/T790M double-mutated EGFR while sparing the wild-type EGFR to prevent an off-target effect is a clinically important problem.…”

“…For example, practitioners elaborate on a known pharmacophore with a plausible potency to design a ligand that forms favorable interactions with pocket residues, achieving higher potency. [31][32][33] Thus, the concepts of SARs and protein-ligand interactions can act as a suitable prior knowledge to improve the generalizability of the ligand design process while providing explainable reasoning. Nevertheless, current approaches overlook protein-ligand interactions during the generation processes, barely considering them.…”

Roles of ubiquitin‑specific protease 13 in normal physiology and tumors (Review)

“…In lung cancer, the relationship between USP13 expression and prognosis is associated with its pathological type. USP13 promotes the proliferation of small cell lung cancer (SCLC) ( 44 ). Epigenetic alterations in the USP13 gene have been identified in certain cancers, such as hypermethylation in embryonal carcinomas of the testis ( 45 ).…”