Molecular Docking Technology, the Key Technology of Structural Molecular Biology

Molecular biology is the science of studying life phenomena and the essence of life at the molecular level. The molecular biology technology provided by some molecular biology service organizations is a more advanced and cutting-edge technology in life science research. Molecular docking is a key technology in structural molecular biology and has played an increasingly important role in computer-aided drug design in recent years. Molecular docking technology is a computer-based analysis that can apply mathematical, biological and computer models to predict the affinity of small molecules for specific receptors.

Molecular docking technology can predict the binding affinity of new chemical entities (NCEs) or drugs based on their chemical structure. In the field of innovative drug research, computer-aided drug design technology, which combines computer technology, optimization methods and drug design, plays an important role. The research of drug molecule docking method is an important link and step of computer-aided drug molecule design.

Molecular docking refers to the placement of small molecules (ligands) on the binding sites of macromolecular targets (receptors) through computer simulation, and the continuous positioning and search for the best matching state within the binding sites according to spatial conformation and interaction. The discovery of new drugs often requires a lot of manpower and material resources, and is a very challenging process. Molecular docking is often used in drug screening. Studies have found that the docking energies of targets and ligands with different structures are different. This is because the structure of the target point is different, which changes a variety of factors that affect the docking process, resulting in a change in the docking result. Studies have shown that although the target structure is different, the order of the docking energy between the target and each ligand is the same.

With the development of science and technology, more and more protein crystal structures have been resolved, providing a large number of targets for compound screening using molecular docking technology. Simulation analysis through molecular docking technology can obtain the docking results of the candidate compound and the protein and the interaction relationship between its functional regions, thereby predicting the target point of the drug, laying a foundation for exploring the mechanism of the compound, and also for using the lead compound The development of new drugs provides a theoretical basis.

Computer-aided drug design technology is playing an increasingly important role in drug research and development with its advantages of economy, speed and efficiency. Medicilon’s Structural Biology Laboratory is equipped with a molecular cloning room and a drug discovery and screening platform based on protein crystallography to support the development of drugs based on structure, from the confirmation of new targets to the final structure confirmation. Medicilon’s structural biology platform is one of the structural biology platforms established earlier in China, and has been identified as an important new drug research and development platform by the Shanghai Municipal Government.

As a key technology of computer-aided drug design, molecular docking has become an important method in drug development. There are three main types of molecular docking technology:

(1) Rigid docking:

The conformation of the target molecule and the ligand molecule does not change during the docking process, only the spatial position and posture of the molecule change. This method is simple in calculation and fast in calculation speed. It is suitable for the calculation of docking between macromolecules with relatively large institutions, and the calculation results are not accurate enough.

(2) Semi-flexible docking:

Semi-flexible docking is a commonly used method in the process of drug screening. During the docking process, the conformation of the target molecule does not change, and the conformation of the ligand molecule changes within a certain range. This method is suitable for the docking calculation between large molecules and small molecule compounds. The calculation is small and the speed is faster.

(3) Flexible docking

The conformation of the target molecule and the ligand molecule can change during docking. The docking method has a large amount of calculation, accurate calculation, and slow speed, and is suitable for accurately studying the identification of molecules. It has been reported that the docking results obtained by treating the ligand and the receptor as a flexible structure are more accurate.

In short, in the field of drug development, molecular docking technology is widely used. On the one hand, molecular docking technology can predict the binding mode between proteins and explore the three-dimensional structure of the binding of two proteins. On the other hand, molecular docking can also be used for virtual screening of large-scale compounds. By sorting the docking results, small molecule compounds with optimal affinity can be screened, and the hypothesis of how ligands can inhibit the target protein can also be proposed. The optimization of the compound is very valuable.

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