Figure 2A shows the Root Mean Square Deviation (RMSD in ?) (blue line), Radius of Gyration (Rodrigues & Bonvin, 2014) (RoG in ?) (orange line), Surface Accessible Surface Area (SASA in ?2) (gray line) and the number of H-bonds (yellow line) versus time in nanoseconds. have been tested against MERS CoV RdRp using molecular modeling and docking simulations, from which four are novel compounds. Molecular Dynamics Simulation for 260 nanoseconds is performed on the MERS CoV RdRp model to test the effect of protein dynamics on the binding affinities to the tested nucleotide inhibitors. Results support the hypothesis of using the anti-polymerases (Anti-HCV drugs) against MERS CoV RdRp as a potent candidates. Besides four novel compounds are suggested as a seed for high performance inhibitors against MERS CoV RdRp. Communicated by Ramaswamy H. Sarma and equilibrated by Molecular Dynamics Simulation (MDS). Materials and methods Sequence retrieval and alignment MERS RdRp structure has not been solved experimentally yet. Therefore, we utilized a molecular modeling approach to construct the all atoms 3D structure of JNJ0966 MERS CoV RdRp. The protein database of the National Center for Biotechnology Information (NCBI) was used to retrieve the sequences for the polymerases of all human coronaviruses (MERS, SARS, HKU1, OC43, NL63, and 229E) (NCBI, 2020). Multiple sequence alignment was done using CLUSTAL Omega web server (Sievers et al., 2011) to reveal the sequence conservations among the downloaded sequences for human coronaviruses and HCV polymerase sequences (PDB ID: 2XI3). ESPript 3.0 software is utilized to prepare the multiple sequence alignment (Robert & Gouet, 2014). Structural alignment of the MERS CoV RdRp model and HCV polymerase structure (PDB ID: 2XI3) was done by the aid of Chimera software (Pettersen et al., 2004) (Root Mean Square (RMS) difference of 2.7??). Structure prediction and docking study I-TASSER web server was used in this study to build the all-atoms 3D structure of MERS CoV polymerase from the sequence (ID “type”:”entrez-protein”,”attrs”:”text”:”AHY61336.1″,”term_id”:”627792519″,”term_text”:”AHY61336.1″AHY61336.1) (Yang et al., 2015). Different protein modelling webservers were used to build the 3D structure of MERS HCoV RdRp, while the model built by I-I-TASSER was the best model based on structural validation servers (Elfiky et al., 2017). The structure was validated using the Ramachandran plot, ERRAT, PROVE, and verify-3D software from Structural Analysis and Verification Server (SAVES) (Hooft et al., 1996; Laskowski et al., 1996; SAVES, 2020). Guanosine triphosphate (GTP), Uridine triphosphate (UTP), IDX-184 (GTP derivative), sofosbuvir (UTP derivative), ribavirin (wide acting antiviral drug), and four suggested guanosine derivatives (Elfiky & Elshemey, 2018) were sketched using SCIGRESS 3.0 tools (Summers et al., 2012). The structures were optimized classically using the MM3 force field (Lii & Allinger, 1989) then were further optimized using semi-empirical parameterization methods 6 (PM6) (Stewart, 1991). Finally, the quantum mechanical density functional theory (DFT) was used to optimize the ligands structure (Becke, 1993). The quantum mechanical functional B3LYP was also used to calculate the infrared transition spectra of the optimized ligands to ensure reality (Saleh et al., 2014). AutoDock Vina (Morris et al., 2009; Trott & Olson, 2009) was employed in this study to assess the binding affinities and possible binding modes of the interactions between the ligands and MERS CoV RdRp. Four nucleotide inhibitors (based on JNJ0966 anti-HCV drugs (guanosine inhibitors)) are utilized in this study. Sofosbuvir, IDX-184, and ribavirin were also tested against MERS CoV polymerase. AutoDock Tools (ADT) software is used to prepare both the small molecules and the protein 3D-structures for the docking experiment. The grid box was set to be 30??30??30?? and its center is selected to be between your residues, D255 and D256. Versatile ligand within a versatile energetic site docking approach can be used within this scholarly study. Furthermore, the Vina credit scoring function is put on score the causing complexes. The docking research is executed using different conformations from the proteins corresponding JNJ0966 towards the proteins at different dynamical state governments (every 10?ns) through the Molecular Dynamics Simulation (MDS) work (Leach, 2001). Molecular dynamics simulation research To guarantee the binding from the ligands inside the MERS CoV RdRp, we utilized molecular dynamics simulation for 260 nanoseconds to guarantee the equilibration from the proteins program since any adjustments in the Cd8a framework can affect the tiny molecule binding. NAMD software program (Phillips et.