Reverse Docking Service

The classic drug design idea is to design compounds that can bind to a given target. The idea of reverse docking is just the opposite. The technology is to dock a compound with known biological activity with the three-dimensional structure of all binding sites in a given protein database, and the protein that can be docked is further verified by experimental methods.

Overall solutions

The main steps of using reverse docking and biotechnology for target identification are:

• Screen out all small molecule compounds with clear biological activity to match each other protein.
• Analyze these proteins and screen out candidate targets according to certain algorithms point.
• Verify the target through biochemical or cell experiments.
• The structure of the complex formed by the protein verifies the existence of docking at the atomic level. The entire process requires a large number of proteins with known structures. Protein structure usually comes from protein database.

Precautions

• PDB Code: The PDB structure code used for docking. You can put the coordinate file generated by docking and the corresponding PDB structure together to observe the interaction mode. It is recommended to use software such as pymol or chimera.
• Affinity Score: The predicted binding affinity, in pKd, which is the scoring result.
• Crash Score: The bump between the docked pose and the target point, the maximum value is 0, especially the smaller such as -5, which means the result is not credible.
• Polar Score: It is the hydrogen bond, salt bridge or coordination interaction between the predicted pose and the target.
• Surface Similarity: The predicted surface similarity between the pose and the complex ligand, the maximum value is 1, the minimum value is 0, the larger the surface similarity to the complex ligand molecule.
• Gaussian Shape: For the predicted similarity of the Gaussian molecular shape between the pose and the complex ligand, the maximum value is 1, and the minimum value is 0. The larger the shape, the more similar the molecular shape of the complex ligand molecule.

AI-based reverse docking

Unlike traditional molecular docking, AI-based reverse docking is used to identify receptors for a given ligand in a large number of crystal structures. It can be used to discover new targets for existing drugs and natural compounds, reposition drugs to replace drug indications, and detect adverse drug reactions and drug toxicity. Generally, AI-based reverse docking (drug relocation) to perform drug relocation requires the following steps:
(1) data set collection;
(2) data set partition;
(3) calculation and modeling of molecular descriptors;
(4) Overall learning;
(5) Retrospective screening activities;
(6) Establish a positive predictive value surface and select an appropriate score threshold;
(7) Prospective virtual screening;
(8) Molecular docking;
(9) Reverse docking score.

Figure 2. AI assisted reverse docking.( Liu B, et al. 2019)

Advantages of reverse docking

• Reverse docking is used to identify the target of a given ligand in a large number of receptors.
• Reverse docking can be used to discover new targets for existing drugs and natural compounds, explain the molecular mechanism of drugs and relocate drugs, find alternative indications for drugs, and detect drug adverse reactions and drug toxicity.
• In reverse docking, the necessary process is similar to the forward docking method: preparing the data set, finding the ligand pose, and scoring and sorting complex structures.
• The significant advantage of reverse docking is that it can not only find targets for pharmacological effects, but also targets that cause toxic and side effects.

Reverse docking provides a list of potential target proteins for further research. Drug target determination is the first step in drug discovery. As one of the strategies to complement experimental methods, reverse docking has become one of the effective tools to determine the potential targets of a given compound, not only for target confirmation, but also for predicting toxicity and adverse effects Side effects can also be used to discover unknown and novel targets for drugs or natural compounds. If you need reverse docking service, please feel free to contact us.