Introduction: Ovarian cancer has the highest mortality of gynecological cancers worldwide. Early diagnosis of ovarian cancer is currently difficult to make in clinical examination, and by the time the diagnosis is made, most tumors have progressed to intermediate and advanced stages with distant metastasis. Biomarkers potentially are used for the early diagnosis of cancers. Aptamers are highly promising molecular recognition elements to develop diagnostic tools especially biosensors for the early detection of cancers. The aim of this evaluation study is in silico molecular docking of single-strand DNA aptamer (designed by Eaton in 2015) and HE4 protein to detect ovarian cancer in its early stages by various software for the design of a novel diagnostic platform. Methods: Molecular docking is a strategy that involves the usage of computer-based simulations to model nucleic acid-target interactions and determined the aptamer-target binding sites. Molecular docking was done using HDOCK server. YASARA was used to analyze specific interaction. Results: Molecular docking showed the specific interaction of HE4 and ssDNA aptamer with the lowest rmsd. Results, revealed interactive sites between HE4 and ssDNA aptamer that only 5 of the 124 amino acids (ASN74, GLN89, GLN96, GLN98 and VAL99) were present in the binding interface with nucleotides (C1, A2, C3, A4, T15, T16, T17, A18, G19, G20 and G21). Conclusion: The results of this study confirmed the interaction and affinity of aptamer model with HE4 protein which can be used for therapeutic and diagnosis application in medicine.
