Abstract A06: Biophysical and biochemical characterization of KRAS G12C inhibition through the SMARTTM platform
Authors: Zhou Minyun , Yuzhakov Alexander , Benod Cindy C , Xue Linlong , Silver Alec D , Iyer Ganesh , Townson Sharon A. , Jin Meizhong , Perl Nicholas R. , Kohlmann Anna , Mann Alan S. , Akcay Gizem , May Earl W. 
Published: June 2021

Abstract
RAS proteins are small GTPases involved in cell proliferation, survival, and differentiation, and are mutationally activated in about a third of all human cancers. These mutations drive cancer by impairing GTPase activity so that the RAS protein is found predominantly in its GTP-bound “on” conformation. Most KRAS isoform mutations are located at codon 12, a glycine in the P-loop of the GTPase active site. KRAS mutations in which the glycine is mutated to a cysteine (G12C) are particularly common in lung cancer. Despite its prevalence as an important oncogene and decades of research, the RAS protein remains an unexploited cancer target. We have developed a novel platform, SMART (Small Molecule Assisted Receptor Targeting), to disrupt the protein-protein interactions of so-called “undruggable” targets. Our compounds bind the immunophilin protein Cyclophilin A (CypA), and subsequently form a ternary complex with the target protein, KRAS. An electrophilic moiety on the ligand selectively forms a covalent bond with the cysteine of GTP-KRAS G12C, thus strengthening the stability of the ternary complex, partially occupying the effector face, and thus occluding the binding of downstream effector proteins, such as RAF. In a separate presentation, we describe a wide breadth of data to support the advancement of a small molecule specifically targeting the activated form of KRAS, with a focus on the cellular pharmacology. In this presentation, we highlight biophysical and biochemical findings that support our novel strategy for targeting GTP-KRAS G12C. SPR reveals the CypA-compound binary KD. A novel SPR protocol method was developed to examine CypA-compound-KRAS ternary complex formation, exploiting the A-B-A injection system of the Biacore 8K. LC-MS is used to characterize the crosslinking of our compounds to KRAS G12C in the presence of CypA, and full kinact/KI analysis is conducted with select compounds; in combination with SPR studies, the noncovalent KD of the ternary complex can be determined. Intrinsic warhead reactivity is measured through GSH adduct formation. TR-FRET studies probe the ability of ternary complexes to inhibit the binding of RAF to KRAS G12C. ITC and BLI are used to confirm ternary complex formation for selected compounds. In addition to guiding SAR, these studies characterize the degree of presenter (CypA) dependence, specificity of compound binding to the G12C mutant and to the GTP nucleotide-bound form of KRAS, and the ability to predict cellular efficacy. Our kinetic crosslinking experiments reveal single-digit micromolar KIs and a good kinact/KI ratio for our compounds relative to published literature on compounds targeting GDP-KRAS G12C. When these values are compared to SPR findings, the noncovalent KD contributes largely to KI, and thus noncovalent interactions play a bigger role in our compound’s interaction with RAS as compared to known GDP-KRAS G12C agents.
Citation Format: Minyun Zhou, Alexander Yuzhakov, Cindy C Benod, Linlong Xue, Alec D Silver, Ganesh Iyer, Sharon A. Townson, Meizhong Jin, Nicholas R. Perl, Anna Kohlmann, Alan S. Mann, Gizem Akcay, Earl W. May. Biophysical and biochemical characterization of KRAS G12C inhibition through the SMARTTM platform [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr A06.