In-silico prediction of compound-protein interaction using computational methods preserves its importance in various pharmacology applications because the wet-lab experiments are time-consuming, laborious and costly. Most machine learning methods proposed to that end approach this problem with supervised learning strategies in which known interactions are labeled as positive and the rest are labeled as negative. However, treating all unknown interactions as negative instances may lead to inaccuracies in real practice since some of the unknown interactions are bound to be positive interactions waiting to be identified as such. In this study, we propose to address this problem using the Quasi-Supervised Learning algorithm. In this framework, potential interactions are predicted by estimating the overlap between two datasets: a true positive dataset which consists of compound-protein pairs with known interactions and an unknown dataset which consists of all the remaining compound-protein pairs. The potential interactions are then identified as those in the unknown dataset that overlap with the interacting pairs in the true positive dataset in terms of the associated similarity structure between interacting pairs. Experimental results on GPCR and Nuclear Receptor datasets show that the proposed method can identify actual interactions from all possible combinations.