E-pharmacophore hypothesis has recently emerged as a useful tool in computer-aided drug discovery and structure-based screening . In Epharmacophore hypothesis, the combination of stereo-electronic features and energetics of a known bound ligand within the complex of its' biological target is measured computationally and later mapped with new ligands. In this study, we used E-pharmacophore model to compare the stereo-electronic features and energetics of our hit alkaloids within M Pro binding site using the complex of the protein with another known non-covalent inhibitor, X77 (N-( . In order to do so, the crystal structure of M Pro bound with non-covalent X77 inhibitor was retrieved from RCSB database and processed as mentioned in the materials and method section to generate the energyoptimized E-pharmacophore model. As a result, total ten pharmacophores were generated having a total 12 non-bond, 4 hydrophobic and 7 hydrogen bond interactions and we selected the pharmacophore having the highest features (AAHHaromHaromHarom where A: Hydrogen bond acceptor, H: Hydrophobic, Harom: Hydrophobic aromatic respectively) for mapping our hit alkaloids (Figure ). The chosen pharmacophore was then screened with alkaloid hits CNP0416047, 3-hydroxy anisotine, and anisotine respectively as one to one mapping based on a cut-off of minimum 4 features. Prior to the mapping, all three alkaloids were structurally optimized using CHARMm force field with Momary-Rone partial charge at pH 7.4 and all possible tautomers, stereoisomers and protonation states were generated. It was found that all three selected alkaloid hits were mapped to '5 features hits' indicating the hit alkaloids displayed the 5 out of 6 features in the mapping with respect to the pharmacophore. Furthermore, the mapping was scored based on a 'fit value' and anisotine displayed the best fit value of 1.50884, whereas CNP0416047 mapped with lowest fit value of 0.644164 with respect to the pharmacophore.