The paper describes a search and selection of potential heparanase inhibitors. This enzyme is inhibited to protect an organism against various diseases such as chronic kidney disease and diabetic nephropathy. These diseases are widely distributed and often lead to death. Searching lowcost plant analogs of compounds which are able to inhibit their target protein activity can make the treatment cheaper and more efficient. The study has been carried out by means of Autodock Vina software to perform molecular docking and Protein Data Bank to obtain a crystal structure. Molecular docking has computed Folate, Folate, Riboflavin to be the most potential heparanase ligands. These compounds are produced by widely distributed plants and known to be harmless to different species.