DOI: 10.5281/zenodo.4067653
title: An in silico docking simulation of SARS Coronavirus2 and Ivermectin

description: <strong>ABSTRACT</strong> COVID-19 is spreading and infecting in the world. And that is occurring a death very much. Of course, I want to cooperate for save peoples. And I was simulating a docking about proteins of SARS Coronavirus 2 in silico. That a papain-like protease, a karyopherin importin α,β and RNA Polymerase. One hypothesis [1] said Ivermectin can destabilises about a bind to an importin and the virus cargo proteins. And I got a significantly results from in silico simulation that at catalytic center of RNA Polymerase. Remdesivir is docking at here. [2] I dedicate this report to a current patients and a future patients. <strong>1. Introduction</strong> The virus is called the bacteriophage. You know that the virus infect the bacteria. Therefore, the bacteria need a counter plan. I think, Ivermectin(Avermectin) is that. One hypothesis, the Coronavirus2 is<br> replicating by using a main protease [4], papain-like protease [4] and this RNA Polymerase. And Ivermectin destablishes about bind to an importin and the virus cargo proteins [1]. I checked for these case. But I<br> seems that Importin is too big for Ivermectin. And netxt, I checked for RNA Polymerase. and I report this result simply. <strong>2. A software for docking simulation</strong> This case is using a software that “Autodock vina” [5]. This software is better performance than other docking simulation softwares. But a simulation accuracy isn’t a high quality more than a real phenomenon<br> yet. This software is using an affinity score [kcal/mol]. See also vina web-site [5]. <strong>3. A docking parameters and Dataset</strong> This case is using following parameters for docking simulations. (1).exhaustiveness: 8<br> (2).num modes: 10<br> (3).energy range: 1 and I was using a protein data PDB:7bzf for RNA Polymerase. And PDB:IVM for Ivermectin. I chosen a chain A from PDB:7bzf by using pymol [8]. And I converted PDB:IVM from .sdf to .pdb by using “PDB<br> format-PDBx/mmCIF conversion service” web-site [9]. <strong>4. Contents</strong> Figure 2: Front view of RNA Polymerase and Ivermectin I tried to a docking simulation during a four monthes about RNA Polymerase (PDB:7bzf) of SARS Coronavirus2 and Ivermectin [6]. And<br> I got a significantly results. I chosen a few higher score to following. mode | affinity | dist from best mode<br> | (kcal/mol) | rmsd l.b.| rmsd u.b.<br> -----+------------+----------+----------<br> 1 -11.5 0.000 0.000<br> 2 -11.1 1.975 3.233<br> 3 -11.0 1.895 2.482 mode | affinity | dist from best mode<br> | (kcal/mol) | rmsd l.b.| rmsd u.b.<br> -----+------------+----------+----------<br> 1 -11.4 0.000 0.000<br> 2 -11.0 1.572 2.041<br> 3 -10.8 4.406 14.971 mode | affinity | dist from best mode<br> | (kcal/mol) | rmsd l.b.| rmsd u.b.<br> -----+------------+----------+----------<br> 1 -11.4 0.000 0.000<br> 2 -10.8 1.550 2.430<br> 3 -10.6 1.648 2.197 These are a near points. You can see a number of rmsd (Root Mean Square Deviation). These are a catalytic center of RNA Polymerase. One paper said [2], this point can combine Remdesivir too. Figure 1,2,3 are a point of best of affinity score that -11.5[kcal/mol]. Of course, If you want to know detail of results then you can download an all eleven data about this simulation from my web-site. <strong>5. Conclusion</strong> I seems that is very significantly result. Because, One, here are a higher score point (Figure 4). Second, here are a catalytic center. Third, Remdesivir can combine at same point [2]. I consider about an accuracy<br> of Autodoc Vina and a conformation will change, probably. You know, this is a computer simulation absolutely. I want to wait a result of cryo-EM and a crystal structure complex. <strong>Acknowledge</strong> Thank you for the NIG supercomputer at ROIS National Institute of Genetics. Because I’m using this computer system everyday.
description: These are a theoretical results. because this is a computer simulation. Therefore, these require a physics experiments. and You can test for examination by using these dataset,. and You can get same results certainly. (This PDF is signed by Japanese Public Key Infrastructure. https://www.jpki.go.jp/)