Various calculations are encompassed in the basic experiments related to drug discovery and preparation, such as the calculation of excited state, charge density, molecular volume and so on. One of the vital and extensively applied computing technologies is virtual screening, which is abbreviated as VS. By utilizing this technology, researchers can search the library of small molecules, thus quickly identifying the structures most probably to combine with drug targets which are usually protein receptors or enzymes. However, as we all know, the quantity of molecules is beyond people’s imagination. Therefore, which correct and sensible method to use for screening compounds is the first problem that experimenters have to consider. Generally speaking, the most commonly used virtual screening methods are ligand-based method, structure-based method and hybrid method.
Ligand-based Method for Virtual Screening
Before explaining this kind of method, we first need to know what the ligands are. According to the definition of Biochemistry and pharmacology, ligand is actually a kind of substance which can combine with biomolecules to construct the complexes. Common small molecules, like ions and proteins, can all act as ligands. The electrons, shapes of molecules and physical and chemical similarities all vary with distinct ligands, which determines the diverse modes of their action on particular molecular receptors or cell lines. In accordance with the shape resemblance or pharmacophore model of the compounds, this approach is able to search the compound database for chemical molecular structures which can match the known active small-molecule compounds. After that, researchers can utilize these picked compounds to build receptor models.
Structure-based Method for Virtual Screening
In addition to the first way to select compounds, there is also a method based on receptors, which is named structure-based virtual screening method, and here the structure refers to the configuration of receptors, which are molecular targets of active ligands. On the basis of the 3D structure of the target protein, researchers adopt this method and molecular docking technology to study the traits of the binding sites and the interaction modes among the targets and small-molecule compounds. Adopting a scoring function related to binding energy, researchers can evaluate the binding ability of protein and small-molecule compounds, and finally select the compounds with reasonable binding mode and high prediction score from numerous compounds for subsequent biological activity testing.
Hybrid Method for Virtual Screening
Although those two methods mentioned above can meet most of the experimental needs, there are still some restrictions. In order to overcome those disadvantages, scientists have developed the hybrid method to conduct screening, which means that the structure and ligand similarities are applied to screen simultaneously. This method mainly utilizes the ligand-binding information, which is based on evolution, to predict small-molecule complexes, but at the same time, in order to ensure the precision of prediction, two other similarities can be considered as well. The first is the global structural similarity, which means that the experimental structure or predicted protein model is used to discover compounds with similar structures to proteins in the PDB holo-template library. And the other is pocket similarity, which is utilized to compensate for the shortage of the first one that cannot recognize the differences in substances showing geometric similarity.
It is a process of high consumption rate whether in terms of time or cost to formally use a drug in the clinical treatment. Therefore, in drug research, any means that can speed up the process and reduce the failure rate will be given priority. By predicting the combination between receptors and ligands, VS technology greatly helps scientists to choose the most suitable compounds in a short time, so it is favored by researchers. In recent decades, this technology has become necessary in drug design.
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