Proof of concept for poor inhibitor binding and efficient formation of covalent adducts of KRASG12C and ARS compounds

by Selleckchem | Jul 21 2023

The use of selective covalent inhibitors with low binding affinity and high reactivity with the target enzyme is a promising way to solve a long-standing problem of the "undruggable" RAS-like proteins. Specifically, compounds of the ARS family that prevent the activation of the GDP-bound G12C mutant of Kirsten RAS (KRAS) are in the focus of recent experimental research. We report the first computational characterization of the entire reaction mechanism of the covalent binding of ARS-853 to the KRASG12C·GDP complex. The application of molecular dynamics, molecular docking and quantum mechanics/molecular mechanics approaches allowed us to model the inhibitor binding to the protein and the chemical reaction of ARS-853 with Cys12 in the enzyme binding site. We estimated a full set of kinetic constants and carried out numerical kinetic analysis of the process. Thus, we were able to compare directly the physicochemical parameters of the reaction obtained in silico and the macroscopic parameters observed in experimental studies. From our computational results, we explain the observed unusual dependence of the rate constant of covalent complex formation, kobs, on the ARS concentration. The latter depends both on the non-covalent binding step with the equilibrium constant, Ki, and on the rate constant of covalent adduct formation, kinact. The calculated ratio kinact/Ki = 213 M-1 s-1 reproduces the corresponding experimental value of 250 ± 30 M-1 s-1 for the interaction of ARS-853 with KRASG12C. Electron density analysis in the reactive region demonstrates that covalent bond formation occurs efficiently according to the Michael addition mechanism, which assumes the activation of the C[double bond, length as m-dash]C bond of ARS-853 by a water molecule and Lys16 in the binding site of KRASG12C. We also refine the kinact and Ki constants of the ARS-107 compound, which shares common features with ARS-853, and show that the decrease in the kinact/Ki ratio in the case of ARS-107 is explained by changes in both Ki and kinact constants.

Comments:

The passage you provided describes a computational study that aims to understand the mechanism of action of selective covalent inhibitors, specifically the ARS family of compounds, targeting the GDP-bound G12C mutant of Kirsten RAS (KRAS) protein. KRAS is a challenging target for drug development due to its "undruggable" nature. The study employs various computational techniques, including molecular dynamics, molecular docking, and quantum mechanics/molecular mechanics approaches, to simulate the binding of ARS-853 to the KRASG12C·GDP complex and the subsequent chemical reaction between ARS-853 and Cys12 in the enzyme's binding site.

By conducting this computational analysis, the researchers obtained a comprehensive understanding of the reaction mechanism and estimated the kinetic constants involved in the process. They performed numerical kinetic analysis to compare the computed physicochemical parameters with the macroscopic parameters observed in experimental studies. Notably, the computational results provide an explanation for the unusual dependence of the rate constant of covalent complex formation, kobs, on the concentration of ARS-853.

The observed dependence of kobs on ARS-853 concentration is found to be influenced by both the non-covalent binding step, characterized by the equilibrium constant Ki, and the rate constant of covalent adduct formation, kinact. The computed ratio kinact/Ki is determined to be 213 M-1 s-1, which corresponds well with the experimental value of 250 ± 30 M-1 s-1 for the interaction between ARS-853 and KRASG12C. Electron density analysis in the reactive region suggests that covalent bond formation follows the Michael addition mechanism, where the C[double bond, length as m-dash]C bond of ARS-853 is activated by a water molecule and Lys16 in the KRASG12C binding site.

Additionally, the study refines the kinetic constants of another compound, ARS-107, which shares similarities with ARS-853. The decrease in the kinact/Ki ratio observed for ARS-107 is attributed to changes in both the Ki and kinact constants.

Overall, this computational characterization provides valuable insights into the mechanism of action of selective covalent inhibitors targeting KRASG12C, shedding light on their binding kinetics and shedding light on the design of potential therapeutics for the "undruggable" RAS-like proteins.