In silico design of a lipid-like compound targeting KRAS4B-G12D through non-covalent bonds

Abstract

One of the most common drivers in human cancer is the peripheral membrane protein KRAS4B, able to promote oncogenic signalling. To signal, oncogenic KRAS4B not only requires a sufficient nucleotide exchange, but also needs to recruit effectors by exposing its effector-binding sites while anchoring to the phospholipid bilayer where KRAS4B-mediated signalling events occur. The enzyme phosphodiesterase-d plays an important role in sequestering KRAS4B from the cytoplasm and targeting it to cellular mem- branes of different cell species. In this work, we present an in silico design of a lipid-like compound that has the remarkable feature of being able to target both an oncogenic KRAS4B-G12D mutant and the phosphodiesterase-d enzyme. This double action is accomplished by adding a lipid tail (analogous to the farnesyl group of the KRAS4B protein) to an previously known active compound (2H-1,2,4-benzothiadiazine, 3,4-dihydro-,1,1-dioxide). The proposed lipid-like molecule was found to lock KRAS4B-G12D in its GDP-bound state by adjusting the effector-binding domain to be blocked by the interface of the lipid bilayer. Meanwhile, it can tune GTP-bound KRAS4B-G12D to shift from the active orientation state to the inactive state. The proposed compound is also observed to stably accommodate itself in the prenyl- binding pocket of phosphodiesterase-d, which impairs KRAS4B enrichment at the lipid bilayer, potentially reducing the proliferation of KRAS4B inside the cytoplasm and its anchoring at the bilayer. In conclusion, we report a potential inhibitor of KRAS4B-G12D with a lipid tail attached to a specific warhead, a com- pound which has not yet been considered for drugs targeting RAS mutants. Our work provides new ways to target KRAS4B-G12D and can also foster drug discovery efforts for the targeting of oncogenes of the RAS family and beyond.

We thank financial support by the Margarita Salas grant which is funded by the European Union – NextGenerationEU awarded to the Universitat Politecnica de Catalunya (Huixia Lu). We also thank financial support by grant PID2021-124297NB-C32 and PID2021-124297NB-C33 funded by MCIN/AEI/10.13039/501100011033, “ERDF A way of making Europe” and given by the “European Union NextGenerationEU/PRTR”. We also acknowledge financial support from Generalitat de Catalunya – AGAUR (grants 2021 SGR 01519 and 2021 SGR 01411). ICMAB is supported by the Spanish Government through the “Severo Ochoa” Program for Centers of Excellence in R&D (CEX2019-000917-S). We thank the CESGA supercomputing center for computer time and technical support at the Finisterrae III supercomputer and the Barcelona Supercomputing Center for support on projects BCV-2023-3-0004 and BCV-2023-3-0005. Molecular graphics made with UCSF Chimera, developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco, with support from NIH P41-GM103311. Zheyao Hu is a Ph.D. fellow from the China Scholarship Council (grant 202006230070).

Peer Reviewed

Postprint (published version)