KRAS(G12C)–AMG 510 interaction dynamics revealed by all-atom molecular dynamics simulations

Abstract

The first KRAS(G12C) targeting inhibitor in clinical development, AMG 510, has shown promising antitumor activity in clinical trials. On the molecular level, however, the interaction dynamics of this covalently bound drug-protein complex has been undetermined. Here, we disclose the interaction dynamics of the KRAS(G12C)-AMG 510 complex by long timescale all-atom molecular dynamics (MD) simulations (total of 75 μs). Moreover, we investigated the influence of the recently reported post-translational modification (PTM) of KRAS' N-terminus, removal of initiator methionine (iMet1) with acetylation of Thr2, to this complex. Our results demonstrate that AMG 510 does not entrap KRAS into a single conformation, as one would expect based on the crystal structure, but rather into an ensemble of conformations. AMG 510 binding is extremely stable regardless of highly dynamic interface of KRAS' switches. Overall, KRAS(G12C)-AMG 510 complex partially mimic the native dynamics of GDP bound KRAS; however, AMG 510 stabilizes the α3-helix region. N-terminally modified KRAS displays similar interaction dynamics with AMG 510 as when Met1 is present, but this PTM appears to stabilize β2-β3-loop. These results provide novel conformational insights on the molecular level to KRAS(G12C)-AMG 510 interactions and dynamics, providing new perspectives to RAS related drug discovery. KRAS is a driver oncogene that is observed particularly in pancreatic, colorectal and lung cancers 1. Most often, KRAS becomes oncogenic by a missense mutation in codon 12 which is coding glycine (G12). From the KRAS G12 missense mutants, G12D and G12V are the most frequent, followed by G12C at the third place 2. In lung cancers, however, smoking-associated G12C mutation is dominating 3,4. Overall, there is a high demand for mutant KRAS targeted therapies 5,6. As a noncatalytic cysteine, G12C is a suitable target for pharmacological intervention via a covalent inhibition of a small molecule drug 7 , providing a potential strategy to target this oncogenic KRAS mutant protein. Since discovery of an allosteric pocket beneath switch-II 8 , determined efforts have been made in the development of G12C targeting covalent inhibitors. Few years later from this initial discovery, a cell-active G12C targeting covalent inhibitor was disclosed 9 , and finally in vivo activity was demonstrated with ARS-1620 10. For more comprehensive overview of covalently reacting G12C targeting small molecules, the reader is recommended a recent review by Goody et al. 11. Currently, G12C inhibitors have reached the clinical trials. The first covalent drug in the clinical development, AMG 510 (Fig. 1A), demonstrated promising antitumor activity 12. Another G12C targeting inhibitor, for which clinical data has been reported, is MRTX849 from Mirati Therapeutics 13. Overall, four KRAS(G12C) targeting inhibitors are currently in the clinical trials. In addition to AMG 510, which is in Phase 1/2 as monotherapy (NCT03600883) and in Phase 1 as combination therapy (NCT04185883 14) and MRTX849 in Phase ...

KRAS Secondary Mutations That Confer Acquired Resistance to KRAS G12C Inhibitors, Sotorasib and Adagrasib, and Overcoming Strategies: Insights From In Vitro Experiments

“…During the development of sotorasib, structural improvements in the quinazoline scaffold to leverage the cryptic pocket formed by H95, Y96, and Q99 in the a3helix of the GDP-KRAS G12C protein produced potent pharmaceutical properties. 18 Pantsar 40 recently reported that Y96 of KRAS G12C forms p-p-stacking, a noncovalent intermolecular interaction between aromatic rings; in addition, R68 formed cation-p interactions, which are derived from an electrostatic interaction between a cation and adjacent electron-rich compounds, with the azaquinazoline base of sotorasib in a molecular dynamics simulation of the KRAS G12Csotorasib complex. In addition, we found that Y96 is located at the entrance of the hydrophobic pocket, where sotorasib and adagrasib bind with the KRAS G12C protein.…”

Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development

“…In this interaction network, hydrophobic hubs (displaying more than three hydrophobic interactions) include the residues V14 and A146, which when mutated are associated with altered RAS dynamics [106,127]. In another study, MD simulations revealed highly dynamic characteristics for the switches even when there exists a covalent inhibitor beneath the switch-II [128]. Importantly, the inhibitor AMG 510 appeared extremely stable regardless of the switch movements.…”

On target: Rational approaches to KRAS inhibition for treatment of non-small cell lung carcinoma

“…Sotorasib is an oral drug that selectively inhibits mutant KRAS G12C by covalently and irreversibly binding to the cysteine in the KRAS G12C transversion, locking the protein in its inactive GDP-bound state ('OFF') (Fig. 2) [78,84,85]. In preclinical testing, sotorasib inhibited ERK phosphorylation and tumor cell growth in multiple KRAS G12C -mutant cell lines in vitro, and in mice with xenografts of human tumor cells [11,86].…”