Modeling the Interplay of Poor Inhibitor Binding and Efficient Formation of a Covalent Adduct upon the Interaction of ARS Compounds with KRASᴳ¹²ᶜ

Abstract

The use of selective covalent inhibitors with a low binding affinity and high reactivity towards 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 activation of the GDP-bound G12C mutant of the Kirsten RAS (KRAS) are in the focus of current experimental research. Here, in the first time we characterize computationally the entire reaction mechanism of formation of the covalent complex between the KRAS G12C •GDP and the ARS-853. 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 with Cys12 in the enzyme binding site. We estimated a full set of kinetic constants and carried out numerical kinetic analysis of the process. We elaborate a strategy 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 complex dependence of the rate constant of covalent complex formation, k obs , on ARS concentrations. The latter depends both on the noncovalent binding step with the equilibrium constant, K i , and on the rate constant of covalent adduct formation, k inact . The calculated ratio k inact /K i = 213 M -1 s -1 reproduces the corresponding experimental value of 250  30 M -1 s -1 for interaction of the ARS-853 compound with KRAS G12C .Electron density analysis in the reactive region demonstrates that covalent bond formation occurs efficiently in accord with the Michael addition mechanism, which assumes the activation of the double C-C bond of ARS-853 by a water molecule and Lys16 in the binding site of KRAS G12C . We refine the k inact and K i constants of the ARS-107 compound, which shares common features with ARS-853, and show that the k inact /K i decreases in the case of ARS-107 is explained by changes in both K i and k inact constants.