DOCKING FUNDAMENTALS FOR SIMULATION IN NANOSCIENCE FUNDAMENTOS DE DOCKING PARA SIMULAÇÃO EM NANOCIÊNCIAS

This work reviews the literature on the molecular docking process, presenting the simulation methodology, the construction parameters and how the results are interpreted. In this context, a study of molecular docking is carried out using the binding protein of the COVID-19 virus with the human cell, called spike, and an antiviral molecule called heparin. As a result, the parameters reached, distances, energies and three-dimensional positioning of the ligand-receptor system are shown. This type of work is currently done in the area of discovering new drugs, or drugs discovered with the aid of the computer. As a final discussion, it concludes the importance of computational knowledge as a way to support various chemical, physical and biological activities in the multidisciplinary field of nanoscience and nanotechnology.


INTRODUCTION
Docking is a class of computer simulation to verify the most adequate molecular modeling to provide a link between a target molecule -usually a protein -and a study molecule, the so-called ligand forming a stable complex (LENGAUER & RAREY, 1996). Molecular Docking techniques aim to predict the best way of binding a ligand to a macromolecule, in this case a protein. Docking consists of the generation of several possible conformations of the ligand in three-dimensional positions of the protein called binding sites (SALMASO & STEFANO, 2018).
Molecular docking is recognized as an effective resource to predict substrate binding with its receptor, some commonly used approaches comprise drug design based on ligand and receptor structure (SINGH et al., 2013). Because the drug discovery and development process is so expensive, molecular docking can reduce the time and resources used in experimental testing.
There are several examples of molecular docking in the literature with biological applications, for example, in (TAVASSOLY et al., 2020), they investigated the compatibility of antiviral drugs in the treatment and blocking of cell entry for COVID-19. According to (SURYWANSHI et al., 2021), they presented a study on the blocking of viral entry into cells, investigating important points of peptides related to the binding of the Spike protein of SARS-CoV-2 with ACE2 (Angiotensin-Converting Enzyme 2).
In the study by (ACHARYA et al., 2019), they performed molecular docking simulations to evaluate some phytochemicals that have actions on proteins belonging to breast cancer (ERα -Estrogen receptor, PR -Progesteron receptor, EGFR -Epidermal growth receptor and mTOR -Mammalian target of Rapamycin), good results were proven for the chosen furanocumarias and the molecular docking tests were validated through in vitro tests.
This work presents the fundamentals involved in molecular modeling and simulation called Docking and how its results can qualify theoretical and experimental work in the field of nanoscience.
In December 2019, Coronavirus disease (COVID-19) was first recognized as a disease caused by severe acute respiratory syndrome (SARS-CoV-2), with the main site of infection in Wuhan, China.
COVID-19 has been a serious threat to global public health with limited treatment. In this context, several researches are being carried out to find an effective treatment against the disease, one of the fastest alternatives being the reuse of existing medicines.
Several drugs are under evaluation to determine the suitability and treat COVID-19, one of these promising compounds being heparin, which is widely used in thrombotic events associated with disease-induced pathology.
The approach chosen to perform molecular docking as an example in this work was the evaluation of heparin (ligand) with the Spike protein of SARS-CoV-2 (receptor), analyzing the points of interaction between the involved parties. Disciplinarum Scientia. Série: Naturais e Tecnológicas, Santa Maria, v. 22, n. 3, p. 67-76, 2021. 69 According to (YUE et al., 2021;WEST et al., 2020), free circulating heparin has an antiviral eff ect and can block the entry of the virus into host cells, as the cellular heparan sulfate binds to the SARS protein -CoV-2 and cooperates with the cell surface receptor angiotensin-2 converting enzyme (ACE2) mediating infection.

METHODOLOGY
Docking basically involves a macromolecule (usually a protein, peptides or a stretch of DNA), called a target and a second structure which is called a ligand. The process of predicting the binding between the target and the ligand is done through the three-dimensional location of the sites that can house the volume of the ligand. This location is done by algorithms that identify the empty space and its probability of biological compatibility.
In a fi rst step, the ligand must be treated, analyzing in its structure places of possible torsion (allowing it to adapt to diff erent spatial conformations, making angular movements in its three-dimensional structure), calculating its electronic charges.
In the next step, the target molecule (receptor) must be treated with the identifi cation of charges, correction of unbound atoms (stabilizing the structure) and solvating the medium with water molecules.
Vina is arguably among the most used programs, probably due to its ease of use and speed when compared to other plug-in programs in the suite and elsewhere, as well as being open source.
In Figure 1 we present the molecular docking methodology used. Disciplinarum Scientia. Série: Naturais e Tecnológicas, Santa Maria, v. 22, n. 3, p. 67-76, 2021. Research groups around the world have modified and built on Vina's source code, improved the search algorithm (QuickVina), made the interface more user-friendly by allowing modification of punctuation terms through the user interface (Smina), and improved the scoring function for docking carbohydrates (Vina-Carb) and halogen bonds (VinaXB), as well as ranking and scoring (Vinardo).
The docking (binding) process at the molecular level that control the coupling ligands to proteins, at the basic level can be described by the laws of quantum chemistry, where the time evolution of molecular systems are expressed in terms of the wave functions of atoms. In practical calculations, however, approximations are used, where the dynamics of the system is defined using atoms represented by point masses that move in the molecular force fields. Molecular forces are determined by electrostatics and chemical bonding interactions between atoms (STAROSOLSKI and POLAńSKI, 2007).
Docking consists of the positioning of the ligand in relation to the target molecule and the binding score based on some metrics, such as scoring functions and the RMSD (Root-Mean-Square Deviation), which is a measure of the average distance -in Ångstroms -between the atoms of the two ligands (target molecule and binding molecule) and is used to measure the quality of the Docking process.
As a metric, the RMSD between the ligand and the receptor must be less than 2 Ångstroms while the affinity value must be as negative as possible (TROTT and OLSON, 2010).

RESULTS AND DISCUSSIONS
In this study, heparin was evaluated, demonstrating that it interacts with the Spike protein of SARS-CoV-2, which is dependent on the cell surface receptor, the angiotensin-converting enzyme 2 (ACE2-angiotensin-converting enzyme 2).

The results of in-silico analysis indicated that heparin interacts with COVID-19 coronavirus
Spike protein 6VYB (WALLS et al.,2020), confirming studies of TAVASSOLY (2020) carried out with similar objectives to this study. The receiver with PDBid 6VYB was prepared by adding hydrogens to the ADT.
The binder used with PDBid 3IRJ was prepared in the ADT software, adjusting its torsion, but its degree of polymerization was changed from 24 to 6 by the author's choice (Figure 2), to solve some compatibility problems of dimension with the Spike protein 6VYB used (Figure 3). In future works we will use different degrees of polymerization to compare the results.

Source: Author
Afterwards, the Autosize Software was used to verify the possible points of affinity between the ligand and the receptor, presenting the following scoring results in Table 1. The first 3 results were presented, but only the first one was used to perform molecular docking. The affinity value for an optimal score (or first place) is the one with the smallest negative value (in kcal/mol) while the RMSD must be less than 2 (Angstroms). In this table, mode 1 is the one calculated with the best disposition in the fit of heparin in the site defined by the docksite with the best possibility of better energy interaction and three-dimensional position. Finally, molecular docking was performed, which presented the following results, described in the sequence through the images of the interaction.

CONCLUSION
The use of computing to study the interactions between different chemical compounds, at the molecular level, with proteins, peptides and stretches of DNA has been a very important strategy in the discovery of new drugs, in the design of new drugs, in the study of the interaction of biomolecules and also in the interaction of nanostructures with complex biological systems.
Using a lot of software with different approaches and after studying the tools, it is possible to achieve different results that serve as a starting point for in vitro and perhaps even in vivo investigations, enabling the optimization of resources to complete the validation of simulation outputs of docking.
The computational use showed an interesting interaction between an antiviral with the spike protein of the SARS-Cov-2 coronavirus, providing a starting point for evaluations with different chemical configurations of heparin, varying in its size, molecular weight and evaluating different configurations to obtain a compound possible to synthesize in the laboratory.