Analysis of the ERK Pathway Cysteinome for Targeted Covalent Inhibition of RAF and MEK Kinases

by Selleckchem | Sep 02 2023

The ERK pathway is one of the most important signaling cascades involved in tumorigenesis. So far, eight noncovalent inhibitors of RAF and MEK kinases in the ERK pathway have been approved by the FDA for the treatment of cancers; however, their efficacies are limited due to various resistance mechanisms. There is an urgent need to develop novel targeted covalent inhibitors. Here we report a systematic study of the covalent ligandabilities of the ERK pathway kinases (ARAF, BRAF, CRAF, KSR1, KSR2, MEK1, MEK2, ERK1, and ERK2) using constant pH molecular dynamics titration and pocket analysis. Our data revealed that the hinge GK (gate keeper)+3 cysteine in RAF family kinases (ARAF, BRAF, CRAF, KSR1, and KSR2) and the back loop cysteine in MEK1 and MEK2 are reactive and ligandable. Structure analysis suggests that the type II inhibitors belvarafenib and GW5074 may be used as scaffolds for designing pan-RAF or CRAF-selective covalent inhibitors directed at the GK+3 cysteine, while the type III inhibitor cobimetinib may be modified to label the back loop cysteine in MEK1/2. The reactivities and ligandabilities of the remote cysteine in MEK1/2 and the DFG-1 cysteine in MEK1/2 and ERK1/2 are also discussed. Our work provides a starting point for medicinal chemists to design novel covalent inhibitors of the ERK pathway kinases. The computational protocol is general and can be applied to the systematic evaluation of covalent ligandabilities of the human cysteinome.

Comments:

The passage you provided describes a research study that focuses on the development of novel covalent inhibitors for the ERK pathway, which plays a crucial role in tumorigenesis (the formation and development of tumors). Although several noncovalent inhibitors targeting RAF and MEK kinases in the ERK pathway have been approved by the FDA for cancer treatment, their efficacy is limited due to various resistance mechanisms.

To address this issue, the researchers conducted a systematic investigation of the covalent ligandabilities (the ability to form a covalent bond with a ligand) of nine kinases involved in the ERK pathway: ARAF, BRAF, CRAF, KSR1, KSR2, MEK1, MEK2, ERK1, and ERK2. They employed constant pH molecular dynamics titration and pocket analysis techniques to study the reactivity of specific cysteine residues within these kinases.

The results of their study revealed that the GK+3 cysteine residue located in the hinge region of RAF family kinases (ARAF, BRAF, CRAF, KSR1, and KSR2) and the back loop cysteine residue in MEK1 and MEK2 are reactive and capable of forming covalent bonds with ligands. The researchers proposed that existing type II inhibitors such as belvarafenib and GW5074 could serve as scaffolds for designing new covalent inhibitors targeting the GK+3 cysteine to achieve pan-RAF or CRAF-selective inhibition. Additionally, they suggested that the type III inhibitor cobimetinib could be modified to target the back loop cysteine in MEK1/2.

The study also discusses the reactivity and ligandabilities of remote cysteine residues in MEK1/2 and the DFG-1 cysteine residues in MEK1/2 and ERK1/2. These findings provide valuable insights for medicinal chemists in designing novel covalent inhibitors specifically targeting the ERK pathway kinases.

Furthermore, the computational protocol used in this study is considered general and can potentially be applied to systematically evaluate the covalent ligandabilities of other cysteine residues within the human cysteinome (the entire set of cysteine residues in proteins).