The avian flu, H5N1, has been the protagonist of every single newscast, newspaper, gatherings, and preoccupations in the world, due to the possibility that this virus, by the moment mortal in approximately 60% of the few human cases known. According to the NHS (National Health Service), the body responsible for health in the UK, and a study carried out in a hospital in Thailand during an outbreak of the disease in 2004 (Apisarnthanarak et al, 2006), catches off guard to the international community in a new outbreak that can kill a lot of people.

The most common symptoms of H5N1 are fever, headache, malaise, myalgia, sore throat, chest pain, stomach pain, vomiting, cough, and rhinitis; and other less unusual symptoms are conjunctivitis, bleeding from the nose and gums, seizures, altered mental state, pneumonia, breathless and other gastrointestinal problems have also been detected, all these symptoms are the one that makes this disease so dangerous, this can be reflected in the statistics of the study carried in Thailand, 67% of the patients infected with the aviary flu died by disease and their symptoms, and according to an article of the Medical News Today, even though the virus is rarely contracted by humans, this disease has been fatal in 60% of infected patients (Brazier, 2020).

Molecular characterization helps to determine the breeding behavior of species, individual reproductive success and the existence of gene flow, the movement of alleles within and between populations of the same or related species, and its consequences (Prasad M., 2014); molecular characterization in the avian flue is used for know-how is that the virus behaves in differents organisms and react to different molecules, to understand the infection and mortality rate that this one has, and after a long research found a cure to the virus by another molecule that counteracts the chemical composition of the virus and change his behavior and stop it and let the white blood cells eliminate the sickness of the receiving body.

In this project, molecular docking of H5N1 will be carried out in humans, trying to unite with an immunoglobulin on a theoretical basis, an investigation of the behavior of the virus that will show the structure to understand the binding of H5N1 with the immunoglobulin visualized in a 3D model.


The principal objective of this project will be the molecular docking of the H5N1 virus through the use of PatchDock, that is gonna be the main tool to use in this project, it was destined to decompose this virus to identify if form a stable complex of the union of the virus to the immunoglobulin.

In the use of PatchDock, some specific pdb files that were obtained from the Protein Data Bank: Biological Macromolecular Structures Enabling Breakthroughs in Research and Education (RCSB PDB). Before trying to bind the virus with the immunoglobulin the virus in hemagglutinin was successfully linked with neuraminidase, since the hemagglutinin molecule recognizes it and if the neuraminidase molecule removes acid from the cell recently invaded by the virus so that the newly synthesized virus can sprout to invade the next cell. Then this pdb file tried to bind to a ligand, but was unsuccessful, tried again, but this time the virus itself with the ligand that worked properly.

After obtaining the finished file, before obtaining this type of file, molecular docking is normally done with PyMOL Viewer Only, that allows visualizing the file that has been download, but, due to the limitations that this tool has and by the purpose of this project this tool is useless, so to be able to fulfill the objective of the investigation; PatchDock is the tool chosen to achieve the goals of the investigation, is gonna be take the same file previously download and do the molecular docking with PatchDock, that has more freedoms for work with the bind of protein, or in our case the bind of the virus H5N1 with immunoglobulin.

To finish, PyMOL Viewer Only was used, which is used to view this molecular docking in 3D. In addition to displaying 3D models in the viewer, the user interacts and manipulates the model and also PyMOL Viewer Only provides an object control panel to adjust the display modes.


Figure 1: Results of the molecular docking*.

In these three figures can be seen the union between the virus H5N1 and immunoglobulins, as can be check in the figures they are three molecules of immunoglobulin(black molecules) and one of the virus(blue molecules).

The findings found against what was expected were totally different, the molecules of the H5N1 virus concerning immunoglobulin didn't bind as expected, an almost perfect union of these two molecules was expected, where very few atoms weren't coupled, but small parts were bound when this molecular docking was completed (approximately 39 atoms joined).

Figure 2: Results of the molecular docking.

Figure 3: Results of the molecular docking*

Having this, and observing that it was necessary to delve more deeply about it, after having carried out this task, it could be determined that said the cause for not having the two molecules totally united, is since the type A immunoglobulin that was used, knowing that it is an antibody, what it does is try to remove completely the disease, in this case, the avian flu, consequently, the immunoglobulin would not finish binding since it would be very risky since the antibodies that bind, contract the disease and the human body would destroy them to prevent its spread or that the disease reappears more adapted to support better the defenses of the receiving body.


To finalize the execution of the molecular docking of avian influenza disease with the antibody, to achieve optimal detection and understanding from 3D modeling, it was completely successful, it were understood the reason for the result of no concrete union between the two proteins, the functioning of antibodies and the H5N1 virus in humans and there was a constant increase in valuable and relevant information throughout this project.

*By Joseph Barbosa Delgado and Diego Herrera Rincón



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