Discovery of a Novel Series of CHK1 Kinase Inhibitors with a Distinctive Hinge Binding Mode

Abstract

A novel series of CHK1 inhibitors with a distinctive hinge binding mode, exemplified by 2-aryl-N-(2-(piperazin-1-yl)phenyl)thiazole-4-carboxamide, was discovered through high-throughput screening using the affinity selection−mass spectrometry (AS-MS)-based Automated Ligand Identification System (ALIS) platform. Structure-based ligand design and optimization led to significant improvements in potency to the single digit nanomolar range and hundred-fold selectivity against CDK2.KEYWORDS: affinity selection−mass spectrometry (AS-MS), Automated Ligand Identification System (ALIS), CHK1 protein kinase, structure-based drug design, thiazole-4-carboxamide C ancer is the leading cause of death globally. 1 Among the treatments used in cancer clinics, DNA-damaging chemotherapies have received widespread use despite their severe side effects on highly proliferative tissues and vulnerability to drug resistance. 2 There is an urgent need in cancer therapy for improved tolerability and longer lasting efficacy. When cells are exposed to agents that induce DNA damage, DNA repair pathways are activated by arresting at various cell cycle check points, G1, S, and G2/M. 3 While normal cells could arrest in the G1 phase through the tumor suppressor protein p53, most cancer cells lack this option because of p53 mutations and will have to rely on the S or G2/M checkpoint for DNA repair and survival. Such reliance in p53 mutant cancer cells would offer a significant opportunity for targeted cancer therapy. 4 CHK1 (checkpoint kinase 1) is a serine/threonine kinase and the key mediator in S and G2/M checkpoints. 5 The abrogation of CHK1 and the remaining checkpoints consequentially will cause cancer cells with DNA damage premature entry into mitosis and result in cell death. 6 Therefore, an enlarged therapeutic window would be expected in anticancer therapies utilizing a combination of a DNA-damaging agent with a CHK1 inhibitor.Over the past years, extensive research efforts in CHK1 inhibition have been undertaken in oncology. Several small molecule CHK1 inhibitors have been discovered and entered into clinical trials. 7−11 In our efforts to discover novel small molecule CHK1 inhibitors, the AS-MS ALIS (affinity selection−mass spectrometry-based Automated Ligand Identification System) platform was used to identify hits from mixture-based combinatorial libraries. 12 ALIS has demonstrated its unique capability in screening label-free mixture-based libraries and finding hits that were subsequently developed into lead compounds in various classes of protein targets, including the anti-infective target Escherichia coli dihydrofolate reductase, 13 antibacterial AccC (acetyl coenzyme-A carboxylase), 14 HCV NS5B (hepatitis C virus nonstructural protein 5B) polymerase, 15−17 protein kinase CDK2 (cyclin-dependent kinase 2), 18 KSP (kinesin spindle protein) in oncology, 19 FABP4 (fatty acid binding protein-4) 20 and the lipid phosphatase SHIP2 (SH2 domain-containing inositol 5-phosphatase 2) 21 in diabetes, MK2 (mitogen-activated protein ...

Structure-based design, discovery and development of checkpoint kinase inhibitors as potential anticancer therapies

“…The SBDD of two new classes of CHK1 inhibitors with high in vitro potency have been disclosed by Merck [49-51]. The thiazole-4-carboxamide 21 was identified using AS-MS ALIS (Affinity Selection-Mass Spectrometry-based Automated Ligand Identification System) (Scheme 1E) [49].…”

Quantum mechanical approaches to structurally informed design

“…Another interesting example of an uncommon interaction is contained in a recently published Chk1 kinase X‐ray structure (PDB code 3u9n) . In this case, the cocrystallized structure of the Chk1 kinase‐inhibitor complex showed a thiazole group acting as a hinge binder with the sulfur atom facing the hinge backbone NH and CO groups (Fig.…”

Automated Assessment of Binding Affinity via Alchemical Free Energy Calculations

“…In the following the checkpoint kinase 1 (CHK1) 68 dataset is described in more detail (cf. Figure 7).…”