Compatibility interactions between the host and the fungal proteins are necessary to successfully establish a disease in plants by fungi or other diseases. Photochemical and antimicrobial substances are generally known to increase plant resilience, which is essential for eradicating fungus infections. Through homology modeling and in silico docking analysis, we assessed 50 phytochemicals from cucumber (Cucumis sativus), 15 antimicrobial compounds from botanical sources, and six compounds from chemical sources against two proteins of Pseudoperonospora cubensis linked to cucumber downy mildew. Alpha and beta sheets made up the 3D structures of the two protein models. According to Ramachandran plot analysis, the QNE 4 effector protein model was considered high quality because it had 86.8% of its residues in the preferred region. The results of the molecular docking analysis showed that the QNE4 and cytochrome oxidase subunit 1 proteins of P. cubensis showed good binding affinities with glucosyl flavones, terpenoids and flavonoids from phytochemicals, antimicrobial compounds from botanicals (garlic and clove), and chemically synthesized compounds, indicating the potential for antifungal activity.