Conformational analysis between 6M71 (SARS COV2 RNA-dependent RNA polymerase) and CHEMBL3120791 using GROMACS Molecular Dynamic simulation.

We analyzed molecular dynamic simulation using GROMACS to study the interaction between SARS-Cov-2 cryo-EM structure of RNA-dependent RNA polymerase (PDB ID: 6M71) and compound CHEMBL3120791 with 20ns simulation using NVIDIA GPU for high performance. SARS Cov2 RNA-dependent RNA polymerase (RdRp) is an enzyme that catalyzes the synthesis and replication of viral RNA from an RNA template. CHEMBL3120791 is in clinical trial for the treatment of HCV (Hepatitis C Virus) infections, and HCV Viruses are like SARS viruses. In our study, we found amino acids LYS47, ASN138, ASN781, THR141, THR710, SER709, SER778, SER784, TYR129 can potentially form hydrogen bonds with the drug molecule. Among all the amino acids mentioned in the list Asparagine 138 and Serine 709 may form hydrogen bonds with CHEMBL3120791 and this interaction can cause changes in conformation between coil and Helix. These amino acids are located around the active site of the enzyme and can be utilized for protein ligand interaction. ASN138, SER709 will actively play and change in conformation during Protein-ligand bond interactions