An in silico docking simulation of SARS Coronavirus2 and Ivermectin

ABSTRACT

    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.

1. Introduction

    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
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
seems that Importin is too big for Ivermectin. And netxt, I checked for RNA Polymerase. and I report this result simply.

2. A software for docking simulation

    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
yet. This software is using an affinity score [kcal/mol]. See also vina web-site [5].

3. A docking parameters and Dataset

    This case is using following parameters for docking simulations.

(1).exhaustiveness: 8
(2).num modes: 10
(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
format-PDBx/mmCIF conversion service” web-site [9].

4. Contents

   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
I got a significantly results. I chosen a few higher score to following.

mode |   affinity | dist from best mode
     | (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
   1        -11.5      0.000      0.000
   2        -11.1      1.975      3.233
   3        -11.0      1.895      2.482

mode |   affinity | dist from best mode
     | (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
   1        -11.4      0.000      0.000
   2        -11.0      1.572      2.041
   3        -10.8      4.406     14.971

mode |   affinity | dist from best mode
     | (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
   1        -11.4      0.000      0.000
   2        -10.8      1.550      2.430
   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.

5. Conclusion

    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
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.

Acknowledge

    Thank you for the NIG supercomputer at ROIS National Institute of Genetics. Because I’m using this computer system everyday.