钙调蛋白-PCAIs结合亲和力的计算机模拟与体外抗癌细胞活力：抗泛突变KRAS药物开发策略

About 90% of pancreatic cancers are pancreatic ductal adenocarcinoma (PDAC), and roughly 90% of PDAC cases are driven by KRAS mutations, which render them very aggressive and resistant to treatments. Therefore, there is a critical need for cancer therapy designed specifically to disrupt and suppress hyperactive G-protein signaling, such as those caused by various mutant RAS isoforms. We previously developed polyisoprenylated cysteinyl amide inhibitors (PCAIs) as potential anticancer agents and showed their efficacies against cell viability, migration, and angiogenesis. We recently identified the pharmacological target of the PCAIs as calmodulin (CALM). To further understand the mechanistic interactions of PCAls with calmodulin, in silico studies were performed. CALM plays a significant role in cancers driven by KRAS proteins. The X-ray crystal structure of CALM with ID 6OS4 and a resolution of 2.05 Å was obtained from the RCSB Protein Data Bank. The crystal structure contained CALM co-crystallized with s-farnesyl-l-cysteine methyl ester (native ligand) and 4 calcium ions. For docking, all water molecules and bound ligands were removed, polar hydrogens were added, and Gasteiger charges were assigned using AutoDockTools. PCAIs were docked onto CALM, and the binding energies were plotted against cell viability EC 50 values obtained using MIAPaCa-2 cells which harbor the KRAS G12C mutation. PCAIs with low EC 50 values also displayed lower binding energies. CALM binds to the farnesylated hypervariable region of KRAS4B. Upon docking analysis, the same key residues were observed in docking interactions between CALM and the PCAIs. Redocking the native ligand produced a binding affinity of -5.9 kcal/mol, while the PCAIs showed stronger affinities that ranged from -8.9 to -6.5 kcal/mol, with similar CALM amino acid to PCAIs interaction patterns. The CALM hydrophobic residues, Leu39, Phe92, Leu105, Leu112, Met124, and Met144, which mediate its association with KRAS4B farnesylated cysteine, also contribute to PCAIs binding. The CALM-KRAS4B interaction is further stabilized through Asp20, Asp22, Asp56, Asp58, and Glu67 residues, which form ionic interactions with the polybasic hypervariable region KRAS4B domain. Although Ser-181 of KRAS4B does not directly contact a specific CALM residue, its phosphorylation state negatively impacts the CALM-KRAS4B interaction, providing an additional regulatory layer to KRAS4B growth stimulation through repulsion of CALM negatively charged residues that attract the polybasic region. Basic N atoms on the PCAIs form defined electrostatic contacts with specific Glu residues of CALM, including N3-Glu14, N4-Glu114, and N4-Glu14, further demonstrating the strong and specific PCAIs disruption of CALM-oncogenic KRAS4B complexation that can be harnessed for effective anticancer drug development.