Property Analysis of Natural Products

In general, compared to synthetic drug and synthetic, drug-like compounds, natural products (NPs) are larger in molecular weight and more hydrophobic. They are also generally more structurally complex, in particular with regard to stereochemistry (number of chiral centers, number of fractions of Csp³ atoms, number of bridgehead atoms in the ring system) and 3D molecular shape. Computational tools are not only useful for physicochemical and structural properties characterization of natural products, but also for quantification of the NP-likeness of compounds by distinguishing NP and NP-like compounds from synthetic compounds with high precision.

BOC Sciences uses cheminformatics expertise to characterize the physicochemical and structural properties of NPs and to compare NPs with other small molecule drugs, drug-like compounds and other types of (organic) molecules. In addition, we also employ various computational tools in natural product design, natural product library design, selection of NPs (and NP derivatives and analogs) from mixed compound collections, and compound prioritization.

Features of NPs

• Cover a much wider chemical space than synthetic compounds
• Exist in chemical space that are often not synthetically accessible
• The structural uniqueness (and complexity) allows for targeting large molecules that would not otherwise be druggable

Figure 1. Screening a Natural Product-Based Library. (Bilal, Z.; et al. 2017)

Our Services

• Rring systems analysis

NPs often show enormous diversity of ring systems, especially aliphatic systems. Regarding the atomic composition, the two most distinguishing features of NPs are the (on average) low number of nitrogen atoms and the high number of oxygen atoms compared to synthetic compounds.

• Distinguishing between NPs from different environments

NPs from different communities have different physicochemical and structural properties:

1. NPs with large rings or aliphatic fatty chains are more commonly to marine species than terrestrial species
2. Bacteria produce many macrocyclic NPs which are characterized by a high proportion of heteroatoms and, associated with this, a high diversity of functional groups
• Assessment of natural product-likeness

BOC Sciences has integrated diverse computational tools to assess the natural product-likeness of compounds in the library:

1. NP-Likeness Score

We use Bayesian statistics to quantify the NP-likeness of compounds based on the similarity of their fragments to known NP fragments.

2. Extended Connectivity Fingerprint (ECFP)

Our teams have applied ECFP to identify NPs and NP-like compounds in a large number of molecules.

3. Random forest classifier

We firstly train this method on a large number of known NP and synthetic compounds. Then, a similarity map is plotted to highlight regions in a molecule that help to predict the molecule as NP or synthetic compound.

4. Natural Compound Molecular Fingerprinting (NC-MFP)

Our teams have introduced NC-MFP method to characterize the structure of NPs based on the scaffolds and fragments they comprise.

BOC Sciences provides professional, rapid and high-quality services of Property Analysis of Natural Products at competitive prices for global customers. Personalized and customized services of Property Analysis of Natural Products 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!