Pathological acid reflux is a common event in patients afflicted with head and neck squamous cell carcinomas (HNSCCs), known to play a role in HNSCC etiology and contribute to complications after surgery or during radiation and chemotherapy. Antacid medications are commonly prescribed in HNSCC patients as part of their cancer treatment, and consist of two classes: histamine 2 receptor antagonist class (H2RA, with cimetidine as its prototypical drug) and proton pump inhibitors class (PPI, with omeprazole as its prototypical drug). Clinical evidence revealed a significant survival benefit of antacid usage in a large cohort of HNSCC patients treated in our Otolaryngology Department, with a median follow-up of over 5 years. Therefore, we postulate that one mechanism by which antacid intake enhances patient survival could involve modulation of tumor cell adhesion to endothelium, critical in the initiation of the metastatic dissemination. This study investigates the potential physical interactions between cimetidine and omeprazole with the endothelial E-selection (E-sel) and its ligand sialyl Lewis X (sLe(x)) using a molecular visualization energy-based program (AutoDock). Docking results were further analyzed with the PyMOL program, which allowed for measurements of the distances between the drugs and the closest interacting atoms or residues on E-sel and sLe(x) molecules. Our model predicts that omeprazole displays a stronger interaction with E-sel than cimetidine, as extrapolated from the calculated overall binding energies. However, the shorter distances existing between interacting atoms in the proposed E-sel/cimetidine complex are suggestive of more stable interactions. Neither antacid/E-sel complex overcame the stronger Autodock-calculated sLe(x)/E-sel interaction, suggesting competitive inhibition was not involved. This study provides the first in silico evidence of omeprazole and cimetidine ability to bind to adhesion molecules involved in tumor dissemination, underlining their therapeutic potential in the HNSCC clinical management.