Reaction-based Enumeration

A diversity of medicinal chemistry studies often require the enumeration of combinatorial libraries based on parent nuclei or chemical reactions, the latter is called reaction-based enumeration, which can help chemists understand the chemical space they can synthesize. Virtual enumeration of chemical reaction is a powerful technique in systematic compound library design or combinatorial chemistry. In reaction-based enumeration, a transformation should first be defined, which is a computational form of the chemical reaction that will be performed on the reactant structure. Reactant structures belonging to the chemical classes defined in the transformation should also be provided.

BOC Sciences’ reaction-based enumeration technique integrates this technology's multiple virtual reaction enumeration engines, enabling the generation of chemically feasible products by performing virtual synthesis without the need for pre-selection of reagents.

Application of Reaction-based Enumeration

• Virtual screening using molecular docking
• Virtual screening using pharmacophore technology
• Virtual screening using molecular shape, electrostatic techniques
• Prediction of compound activity using QSAR or other models

Figure 1. Schematic of the approach to predicting reaction products using enumeration method. (Coley, C. W.; et al. 2019)

Reaction-based Enumeration Process

BOC Sciences can create a virtual library of compounds by simply mapping a reaction route, and the reactants are enumerated by cheminformatics techniques. Each reactant, product can be coded with SMILES1 or characterized in some other format, various groups can be characterized, queried, and counted in quantity with SMARTS2. Reactions can be characterized with SMILES, SMARTS, SMIRKS3, or RXN. Our reaction-based enumeration process is listed as following:

• Defining reactions

In order to perform a reaction-based enumeration, the reaction is firstly defined as a virtual transformation according to which the reactant molecules will combine to form the product.

• Read in the reagent compound database

We identify the compounds in the reagent database using the SMARTS language and calculate the number of groups for each compound.

• Run a virtual synthesis

We create target reactions and generate products in SMARTS language

The results of each enumeration will be added to clients’ database as a new table that will contain the following information:

1. The compound identifier (CdId) of the enumerated molecule
2. The structure generated
3. The number of related products when more products are generated in the reaction
4. The respective reactants
5. The identifier of the reactants and the composite structure
6. The molecular weight and molecular formula of the enumerated structures

• Calculation and filtering of physicochemical properties of the products

BOC Sciences provides professional, rapid and high-quality services of Reaction-based Enumeration at competitive prices for global customers. Personalized and customized services of Reaction-based Enumeration can satisfy any innovative scientific study demands. Our clients have direct access to our staff and prompt feedback to their inquiries. If you are interested in our services, please contact us immediately!