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. the and are like SARS viruses. our study, we found amino acids LYS47, ASN138, ASN781, hydrogen bonds with the drug molecule. C Viral Remdesivir Uprifosbuvir Derivatives Better Inhibitors of SARS Cov2 RNA-Dependent RNA Polymerase Determined Docking Studies.


INTRODUCTION:
SARS -Cov2 has immerged as one of the deadly viruses of the 21 st century and starting late 2019 and beginning of 2020 , COVID-19 has been declared a pandemic effecting not only health of the existing population but also causing economic disasters in several places around the world [1]. SARS -Cov2 is a positive strand RNA virus and replication of its genetic material is crucial to its survival and spread among human host [2]. RNA dependent RNA polymerase is utilized by SARS-COV2 to propagate and spread among human population and is one of the drug targets in treating COVID-19 [3,4,5] .
RNA dependent RNA polymerase or RdRp has been used extensively as a drug target in treatment of COVID-19 [3]. Recently one such drug Remdesivir, which is a nucleotide analogue has proved effective in treatment of COVID-19 in some clinical trials. Remdesivir binds to RdRp and stops viral replication thereby preventing replication and multiplication of virus inside host cells [6,7,8] . RdRp of SARS CoV2 has several non-structured proteins like NSP12, NSP 7 and NSP8 [9,16]. Remdesivir binds to active site residues located in NSP12 molecule of RdRp [10] . Earlier by docking studies we investigated several Remdesivir analogues that can be used as potential drug target in treatment of COVID-19 [11].
In this study, we analyzed CHEMBL3120791 [12] and performed Molecular dynamic simulations of protein drug complex using GROMACS [13] . The structure we used here is Cryo EM structure of RdRp from SARS CoV2(PDB ID 6m71) [14,15] . This drug molecule has been effective against HCV virus and is under clinical trial [17]. The present Molecular Dynamic (MD) simulation studies will provide insights into protein drug interaction and a closer view of the interacting residues present in the active site of RdRp. The dynamics of binding site will be an important step in structure-based drug design of SARS CoV2.

MATERIAL & METHODS:
Based on our docking studies [11], we identified CHEMBL3120791 which is analogues to Remdesivir, is potential binding ligand molecule on (PDB ID 6m71) SARS-Cov-2 cryo-EM structure of RNA-dependent RNA polymerase (RdRp). We have used GROMACS for molecular dynamic simulation. We have used NVIDIA NGC GROMACS 2020.2 and with of NVIDIA 1080 Ti GPU.
We have prepared protein-ligand complex using outputs of Autodock Vina [18] and later PyMol [19] is used to save as PDB file. To fix missing hydrogen or residues of this complex, we used Swiss PDB Viewer [20]. CHARMM force field was added on ligand using swissparam.ch website [21]. For GROMACS commands, you can visit my GitHub link (https://github.com/DSPavan/covid19Research). For our ligand-protein complex of 851 amino acids, for 20ns MD simulation, on 2 GPU, 22 GB RAM, NVIDIA 1080 Ti, it took 26 hour time (more than 1 day).

RESULTS AND DISCUSSION:
We analyzed for active site and interaction between proteinligand, after 20ns Molecular Dynamic simulation. Using Ligplot+ [22], we found that active site is at ASN138 (Fig. 1). We analyzed further for Hydrogen Bond interactions between Protein and Ligand, Results are summarized in Table 1. Amino acids LYS47,  ASN138, ASN781, THR141, THR710, SER709  We analyzed further, for conformation changes during simulation on above amino acids at active sites. From these amino acids, we observed, ASN138 and SER709 only changed during this simulation. This indicates ASN138, SER709 will actively play and change in conformation during Protein-ligand bond interactions.
ASN138 showing changes of conformations from Coil and Helix during simulation as in Fig 2 and Fig 3. Similarly SER709 also changing between Coil and Helix as in Fig 4 and   Most dominantly it is Helix form. Fig , Fig   Fig 5: Changes in SER709 during the simulation. We observed Coil and Helix. Conformational changes are shown using PyMol for visulaizatio

CONCLUSION:
Molecular dynamics using GROMACS with 20ns simulation indicates, Amino acids LYS47, ASN138, ASN781, THR141, THR710, SER709, SER778, SER784, TYR129 which are forming Hydrogen bonds with Ligand. And in this Asparagine 138 and Serine SER709 of PDB ID: 6M71 (SARS COV2 RNA-dependent RNA polymerase) are forming Hydrogen bonds with CHEMBL3120791 and present in active site location clearly there is a change in conformation between coil and Helix. This indicates CHEMBL3120791 inducing and changing the confor mation of a protein RNA-dependent RNA polymerase CHEMBL3120791 which is in clinical trial for HCV can be potentially used for SARS Coronavirus 2. This work can be extended for Free Energy Perturbations (FEP) with 100ns and above for further analysis.