International Journal of Recent Research and Review, Vol.
XI, Issue 3, September 2018
Allicin an Inhibiting Potential of HIV Virus: A Molecular
Docking Studies Comparative with the Ritonavir® Inhibitor
Lucas Lima Bezerra1, Emmanuel Silva Marinho2,Márcia Machado Marinho 3,
1
Department of Chemistry, University State of Ceará, Brazil.
2
Department of Chemistry, University State of Ceará, Brazil.
3
Departamento of Pharmacy, Federal University of Ceará. Brazil
Email- 1aurineide.lima @aluno.uece.br
Abstract – Acquired Immune Deficiency Syndrome
(AIDS) is a disease of a global nature, affecting countless
countries, making several victims over the decades.
About 7,000 people are infected with the virus every 24
hours, where the disease is currently the fifth leading
cause of death among adults. Allicin has been a target
chemical in many studies, due to its strong anti-
bacterial, antifungal and anti-parasitic activity. A
comparative molecular docking study between the HIV-
1 protease virus protein with Ritonavir® and Allicin
was conducted, where nine attractive twists were
obtained for each ligand, and it was possible to see the
reason why the Ritonavir® ligand is used in the
treatment of disease, due to its high affinity and low
molecule rmsd. As for Allicin, it showed a reasonable
affinity and a good rmsd, where from structural
alterations, it is possible to increase the interaction with
the target protein, consequently, it will have a greater
biological activity, being a possible drug for the
treatment of AIDS.
Keywords - Docking molecular. HIV-1 Protease
Inhibitor. Theoretical chemistry.
I. INTRODUCTION
The identification of the acquired immunodeficiency
syndrome in 1981, commonly known as AIDS, became
a milestone in human history. The epidemic of human
immunodeficiency virus (HIV) and AIDS represents a
global, dynamic and unstable phenomenon, whose form
of occurrence in different regions of the world depends,
among other determinants, on individual and collective
human behavior [1]. Over the past 30 years, the AIDS
epidemic has had devastating consequences for
families, communities and countries and is one of the
greatest challenges to public health. More than 7,000
people are infected with the virus every day, and one
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person dies every 20 seconds of an AIDS-related
illness. The disease is currently the fifth leading cause
of death among adults and the leading cause among
women aged 15 to 49 years [2] [3].Sub-Saharan Africa
continues to be the hardest hit with 60% of people
living with HIV in the world, where women represent
58% of this total. The Caribbean, Eastern Europe and
Central Asia, with a prevalence of 1% in the general
population are also areas strongly affected by the
epidemic [4]. Most people living with HIV are entitled
to antiretroviral treatment, but this situation is almost
always unequal, particularly with greater difficulties for
key populations at risk [5].
The AIDS epidemic in Brazil is categorized
according to the parameters considered by the World
Health Organization. In this situation, countries with a
prevalence of HIV infection are less than 1% among
women between the ages of 15 and 49 and more than
5% in subgroups of the population at higher risk [4],
this being the case in Brazil, whose prevalence of HIV
infection in the general population is around 0.6% [6],
and in 5.9% among drug users illicit [7], 14.2% among
men who have sex with men [8] and 4.9% among
women sex workers [9]. Estimates indicate that
approximately 718,000 individuals are living with
HIV / AIDS in Brazil, but only 80% are aware of their
diagnosis. In the last 10 years, the AIDS detection rate
in Brazil has increased by around 2%, with a decrease
in the Southeast and South regions and a rise in other
regions [4].
Allicin is the component responsible for the
characteristic odor of garlic and is a form of defense
against aggressions from outside; not being present in
the intact garlic occurs only when the garlic is
damaged, that is, when it is cut or crushed [10]. Data Bank repository [20], where the protein with the
Allicin, when produced, eliminates fungi and inhibits Ritonavir® ligand was obtained in the same file. Then,
the development of bacteria around them, because due we separated the ligand from the protein, obtaining 2
to its antioxidant power, it causes an instant reaction files at the end of the separation process (protein.pdb,
with the free thiol groups [11], easily penetrating the Ritonavir® .pdb). The second step was to design the
biological cells and deactivating their enzymes [12]. chemical structure of Allicin and then we had the
These features of Allicin give you particularity and structural optimization by mmff94 mechanics in
interest in its importance. Over the years several in Avogadro® software. Then, the preparation of the
vitro studies have demonstrated that Allicin has a protein was performed, where we removed the water
strong anti-bacterial, anti-fungal, anti-parasitic activity residues, added polar hydrogen and saved the files in
against a wide range of microorganisms [13] [14] and PDBQT format, through the AutoDockTools® software
the level of cholesterol and blood pressure reduction [21]. After preparation, we had the realization of the
[15]. molecular docking, from the software AutoDockVina®
Molecular docking provides estimates of the [22].
free energy binding between the protein and the linker,
III. RESULTS AND DISCUSSIONS
even before they are synthesized. The computational
costs of these studies are much lower, when compared In order to perform molecular docking, we used the
to laboratory costs incurred in synthesizing and HIV-1 protease protein (Figure 1) from the Protein
pharmacologically testing various substances Data Bank © repository, where it is registered with the
[16].This important tool has been used to filter access code in the PDB of 1HXW, obtained by X-ray
compounds that are not intended to be targeted, and to diffraction : 1.8 Â and R-Value Work: 0.201). The
design the possible candidates who would have a good three-dimensional structure of the ligands, Ritonavir®
interaction with the active site of the receptor [17]. (Figure 2A) was obtained from the PubChem®
From the molecular anchorage, different repository (https://www.ncbi.nlm.nih.gov/)(PubChem
spatial conformations of the ligand are obtained, CID: 392622) and from the Allicin ligand (Figure 2B).
allowing the analyst to identify which of these is the in the chemspider repository
most probable in the target ligand interaction. From (http://www.chemspider.com), ChemSpider ID: 58548
each spatial conformation, free energies of binding .
(between binder and target) are obtained, where the
lowest energy is considered the most probable to
justify the conformation of the interaction [18].
The interactions between the drug and
proteinaceous target occur through intermolecular
forces of the induced and dipole-type dipole type.
Among the permanent dipole-dipole forces the most
common in these systems are the hydrogen bonds, the
induced dipole-dipole may be forces of Van Der
Waals or London [19]. The objective of this work was
to perform a comparative docking between HIV
protease virus protein and Ritonavir® ligands, used in
the treatment of AIDS and Allicin.
II. METHODOLOGY
Fig.1. Structure of virus protein HIV-1 protease (1)
In this work we used free access software based on the
Windows operating system. The first step was to obtain
the structure of the HIV virus protein from the Protein

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 Table II
Attractive docking twists with Allicin

Mode Affinity Rmsd u.b Rmsd l.b

1 -3.7 0.000 0.000
2 -3.7 4.634 6.270
3 -3.7 1.958 5.358
4 -3.6 5.115 1.682
Fig.2. Chemical structure of the ligands Ritonavir® (A) and
5 -3.6 1.338 3.799
Allicin (B)
6 -3.6 2.851 4.856
After the two docking, nine attractive twists were 7 -3.5 1.724 4.856
obtained for the two ligands with the virus protein 8 -3.4 2.517 2.657
(TABLE I and II). From the results obtained from the 9 -3.3 2.529 5.732
docking, an analysis of all the attractive twists obtained
for the two ligands was made, where Ritonavir® After the analysis of the attractive twists, we obtained a
presented the torsion 4 with affinity of -7.9 kcal / mol. distance of 2,701 Â °, between the target protein and
(rmsd) is the measure of the average distance between Ritonavir®, where it was possible to visualize that the
the atoms (usually the backbone atoms) of oxygen atom (4) was interacting with the amino acid
superimposed proteins, the Ritonavir® presented a ILE 50.A HN of the protein, (Figure 3).
value of 2,004 (rmsd ub) and 2,884 (rmsd lb) . As for
Allicin, we had torsion 8 of -3.5 kcal / mol affinity,
rmsd u.b. 2,517, rmsd l.b 2,657. Remembering that
rmsd should present the value between 2.0 to 2.5 for
docking to be considered valid, if it shows rmsd less
than the values mentioned, it means that the connection
mode is with high probabilities of being correct.

Table I
Attractive docking twists with Ritonavir®

Mode Affinity Rmsd Rmsd

Fig. 3. Distance of binding between the HIV-1 protease
l.b u.b
protein and the Ritonavir® ligand.
1 -9.4 0.000 0.000
2 -8.5 3.410 11.305 Then, we obtained the value of the protein binding
3 -8.2 4.373 9.562 distance with Allicin, in the amount of 3,473 Â °, and it
4 -7.9 2.004 2.884 was possible to visualize that the Carbon atom (2) was
5 -7.8 4.661 8.261 interacting with the ILE 50.B HN amino acid of the
6 -7.0 5.202 10.017 virus protein (Figure 4).
7 -7.0 5.285 9.380
8 -7.0 4.897 9.000
9 -6.9 6.279 11.784

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Fig. 4. Distance of binding between the HI-1V protease
protein and the Allicin ligand.
IV. CONCLUSIONS
From the molecular docking between the target protein
and Ritonavir® , we had confirmation of why it is used
directly in the treatment of the disease because of its
optimal affinity, its low rmsd and its interaction
distance. As for the docking between the same protein
and the Allicin ligand, it was possible to visualize that it
presented excellent rmsd values, indicating it as a
possible drug for the treatment of AIDS, in order to
obtain even better interactions, it will be necessary to
make some structural changes in search of better
biological activity.
V. ACKNOWLEDGMENT
The State University of Ceará (PROPGPQ / UECE) for
the support. This work was partially supported by the
Cearense Foundation for Science and Technology
Support (FUNCAP), the Coordination for the
Improvement of Higher Education Personnel (CAPES).
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