Warhead-bearing natural compounds for multi-pathway irreversible inhibition to overcome drug resistance in colorectal cancer.

Abstract

Colorectal cancer (CRC) remains the second leading cause of cancer-related deaths globally, with approximately 930000 fatalities recorded in 2020. Resistance to conventional therapies continues to be a major obstacle in colorectal cancer treatment, highlighting the need for novel therapeutic strategies to enhance efficacy. This study aims to bridge this gap by exploring a multi-target inhibition approach using naturally derived electrophilic compounds, offering a potential solution to overcome drug resistance. Key CRC-covalent targets-EGFR, SRC, AKT1, HER2, and ERK2-were identified through network pharmacology and protein-protein interaction analysis. A panel of natural compounds, including ophiobolin A, deoxyelephantopin, eupalmerin acetate, curcumin, andrographolide, and syringolin A, was assessed for their inhibitory potential, benchmarking their activity against reference chemotherapeutics. Covalent docking and covalent molecular dynamics (CMD) were performed for 30 ligand-protein complexes to evaluate the binding affinities of the studied compounds. Against EGFR, curcumin displayed a competitive docking score of - 9.458 kcal/mol and ΔG_bind of - 23.00 kcal/mol, closely matching the performance of afatinib (- 10.134 kcal/mol and - 24.28 kcal/mol, respectively). Syringolin A and andrographolide also exhibited strong binding affinities for EGFR. Against SRC, curcumin and andrographolide demonstrated excellent binding potential, achieving docking scores of - 8.360 and - 6.585 kcal/mol and ΔG_bind values of - 38.91 and - 34.00 kcal/mol, respectively. In the case of AKT1, andrographolide displayed a competitive performance (- 8.044 kcal/mol, ΔG_bind: - 32.00 kcal/mol), followed by curcumin and syringolin A. Andrographolide achieved the strongest binding affinity among the natural compounds against HER2 (- 7.006 kcal/mol, ΔG_bind: - 21.01 kcal/mol) and ERK2 (- 7.640 kcal/mol, ΔG_bind: - 33.00 kcal/mol), outperforming curcumin (- 7.468 kcal/mol, ΔG_bind: - 31.23 kcal/mol) and deoxyelephantopin (- 6.517 kcal/mol, ΔG_bind: - 29.01 kcal/mol). These results underscore the strong binding affinities of natural compounds to CRC targets and suggest that these compounds, either as standalone agents or in combination therapies, could complement existing chemotherapeutics by overcoming treatment resistance, thereby improving therapeutic outcomes in CRC patients.