# Computer-Aided Drug Design Boosts RAS Inhibitor Discovery
## 3 Application of CADD Methods in the Development of RAS Inhibitors
### Molecular Docking Studies  
As the most common method in the structure-based drug design of CADD, molecule docking is widely used in RAS-targeted drug discovery. The basic principle of molecule docking is to give a prediction of the ligand-receptor complex structure by computation methods. To achieve this aim, there are two key steps: sampling and scoring. The former targets ligands and active sites of proteins; moreover, it estimates experimental binding modes; the latter evaluates binding affinity through a scoring function (with various assumptions and simplifications) [85]. The earliest reported docking method is called \"rigid body docking\" derived from [PERSON]'s \"lock-and-key assumption\". The essence of rigid body docking is that both ligands and receptors are treated as rigid bodies and that the affinity between ligand and receptor is positively related to the geometric fit between their structures [86]. This method is still used for macromolecular interactions due to its simplicity and feasibility. However, in practical tests, rigid body docking procedures such as ClusPro produced obvious disadvantages, such as fewer hits as the top 1 prediction and the lower accuracy of the generated models [87]. Over time, the theory of \"induced-fit\" was developed. It states that the active site of the enzyme is non-rigid. The substrate can induce a corresponding conformational change of the active site of the enzyme, and the relevant groups rearrange the correct orientation so that the enzyme and substrate fit together to form an intermediate complex, causing a reaction [88]. As a developmental method, \"flexible docking\" allows the conformational changes of small molecules or targets to precisely examine intermolecular recognition by matching spatial shape and energy. The binding capacity is ultimately determined by the change in binding free energy (\(\Delta\)Gbind) during the formation of the complex with indispensable kinetic considerations [89]. To simplify biological macromolecular dynamics, the assumptions of additivity and transferability have been employed in force fields instead of electronic degrees of freedom. Most classical force fields focus on five terms: the bond deformation and the angular geometry (stretching/compression of bonds, angular bending), rotation around some dihedral angle (torsion), the so-called nonbonding, the electrostatic interactions, and the dispersive interactions, as well as the repulsion because of atoms overlapping (van der Waals forces). The extended complex force fields include atomic polarizability and coupling forces, for instance, cross-coupling between bonds and angles [90]. In the history of RAS-targeted drug discovery, molecular docking technology has screened an indirect inhibitor to inhibit RAS nucleotide exchange. By constructing a series of KRAS conformers containing infrequencies and performing blind docking with AutoDock4.2, a bicyclic diterpene lactone from andrographis paniculate andrographoides (AGP) was identified. Its benzylidene derivatives can bind to a transient pocket on KRAS to block the exchange of GDP-GTP and thus inhibit the signal transduction of KRAS. The successful inhibition study not only suggests that nucleotide exchange factors are required for RAS signal transduction but also demonstrates that the inhibition of nucleotide exchange is a practical approach to abolish the function of oncogenic RAS mutants [91]. In RAS post-translational modification, processing required three enzymes, as mentioned earlier, so targeting one of these enzymes is undoubtedly a promising strategy for inhibiting the process [92]. Molecular docking uses the crystal structure of FIase as a template to clarify the interaction between antroquinonol and the CAAX box of FIase after verifying the inhibition of isoprene transferase by antroquinonol in vitro. In conclusion, antroquinonol can inhibit the activity of prenyltransferase to restrict the activation of RAS and RAS-related GTP-binding protein, leading to the activation of autophagy and death of the cancer cell [93].