Xiang Zhai, Richard A Ward, Peter Doig, and Argyrides Argyrou
Biochemistry 2020
DOI: 10.1021/acs.biochem.0c00104
Osimertinib is a covalent, third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) approved for treating non-small cell lung cancer (NSCLC) patients with activating EGFR mutations (Exon19del or L858R), or with T790M resistance mutation following disease progression on first- or second-generation EGFR TKIs. The aim of this work was to understand how osimertinib achieves selective inhibition of mutant EGFR relative to wildtype through evaluating its kinetic mechanism of action. In doing so, we developed methodologies combining steady-state and pre-steady-state kinetics to determine the covalent inactivation rates (kinact) and reversible binding affinities (Ki) of osimertinib for WT, L858R and L858R/T790M EGFR, and compared these data to the inhibition kinetics of earlier generations of EGFR TKIs. The kinact/KI values indicate that osimertinib inactivates L858R and L858R/T790M with 20-fold and 50-fold higher overall efficiencies compared to WT, respectively. The Ki values reveal that osimertinib binds 3-fold and 17-fold tighter to L858R and L858R/T790M than to WT, respectively, while the kinact values show that osimertinib reacts 3-fold faster with L858R and L858R/T790M than with WT EGFR. We conclude that osimertinib achieves selective inhibition of L858R and L858R/T790M through improved affinities and improved rates of covalent bond formation via better positioning of the acrylamide warhead. This work highlights the importance of optimizing both reversible drug-target interactions and the inactivation rates for covalent inhibitors to achieve selectivity targeting mutant EGFR.
A blog highlighting recent publications in the area of covalent modification of proteins, particularly relating to covalent-modifier drugs. @CovalentMod on Twitter, @covalentmod@mstdn.science on Mastodon, and @covalentmod.bsky.social on BlueSky
Linking of fragments in neighboring binding sites is one of the optimization strategies in fragment-based drug discovery, where additive or even more substantial bioactivity improvements can be realized. However, such efforts present a considerable challenge when one fragment binds covalently to the target protein, as small modifications can influence the correct positioning of the covalent warhead toward the targeted nucleophilic residue. Here, we present a case study of fragment linking that yielded single-digit micromolar, covalent inhibitors of the SARS-CoV-2 main protease, starting from fragments that were inactive in the biochemical assay. Using structural information from a recent, high-throughput crystallographic fragment screen, we show that the success of fragment linking in the design of targeted covalent inhibitors is heavily impacted by several factors, including the warhead type, the labeling chemistry, and even subtle changes in the designed linker. Notably, we observe that induced fit effects might override the original fragment orientations in the linked molecule, highlighting the need for reliable structure verification, especially in consecutive rounds of fragment elaboration.
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