Combining Ligand- and Structure-Based Approaches to Develop Haloacetamide-Derived Di(hetero)arylmethanes as Potential Anticancer Agents

The convergence of ligand-based and structure-based computational strategies provides a robust foundation for hit optimization in anticancer drug discovery. We integrated ligand-based SAR with structure-based covalent docking to guide the optimization of haloacetamide-derived di(hetero)arylmethanes. SAR revealed that the 2-haloacetamide warhead is essential, while the di(hetero)aryl scaffold modulates activity, leading to submicromolar bis(pyrazolyl)methane hits. Rather than seeking to establish a definitive molecular target, we used GAPDH and GSTO1 as experimentally motivated target hypotheses to derive structural constraints for covalent scaffold design. Covalent docking was used to prioritize these hypotheses and guide the design of phosphorylated diarylmethane derivatives, leading to the identification of highly cytotoxic bromoacetamide compound, comparable to doxorubicin. In PANC-1 cells, this lead decreased LDH activity and increased PDH activity, suggesting a shift in cellular metabolism from glycolysis toward oxidative phosphorylation. The results demonstrate the utility of target-hypothesis-guided design under conditions in which molecular target identity remains unresolved.