Structural Diversity Assessment of Natural Products

Compared to other synthetic compounds, natural products (NPs) possess higher structural diversity, which can be reflected at the fragment level. Most studies on the assessment of structural diversity of NP have compared them to synthetic compounds by introducing the concept of molecular frameworks (scaffolds). Currently, scientists are working on the visualization of scaffolds characteristic to NPs and comparing them with those of synthetic compounds. In addition, multiple rule-based approaches are developed to provide different perspectives for NP diversity analysis. This method allows for automated assignment and evaluation of major NP classes.

BOC Sciences have integrated a diversity of softwares and computational tools to assess the structural diversity of natural products, aiming to deliver a natural product library containing compounds with high structural diversity.

Figure 1. Chemical diversity analysis of natural products targeting aging-associated proteins. (Fang, J.; et al. 2017)

Our Services

At BOC Sciences, a series of methods are employed to visualize the chemical space of a NP compound, helping to analyze the structural diversity.

• Scaffold Hunter

Scaffold Hunter is designed based on molecular scaffolds and multiple clustering algorithms, and we use this powerful tool to visually analyze the structural diversity of NP compounds in our compound libraries.

• Principal component analysis (PCA)

BOC Sciences supports both molecular fingerprint-based PCA and physicochemical property descriptor-based PCA to map the chemical space of natural products in the library.

• ChemGPS

We project new structures into the ChemGPS based on the predicted PCA scores and then map the chemical space of small molecules, generating results that can be used for subsequent prediction of action mode and structure-activity relationship analysis.

• Self-organizing maps & generative topographic map

At BOC Sciences, these two methods are also frequently used to compare the molecular structure of NPs with those of drugs, and to visualize the structural diversity of fragment-sized and non-fragment-sized NPs.

• T-distributed Stochastic Neighbor embedding (t-SNE) & Unified Manifold Approximation and Projection for Dimension Reduction (UMAP)

t-SNE and the recently introduced UMAP methods can produce accurate visualizations that are superior to those from PCA.

• Consensus diversity graph (CDP)

We have developed CDP to accurately present the median (or other) values of some key properties of a compound (e.g., physicochemical properties, molecular diversity, scaffold diversity).

• Statistical-based database fingerprint (SB-DFP)

The SB-DFP based on individual fingerprints is able to represent the chemical space of a compound database. The SB-DFP is generated by comparing the binomial distributions of molecular fingerprint features selected from compounds in the dataset of interest and that of a reference dataset. In addition, we also apply SB-DFP approach to evaluate and visualize the similarity of the chemical space of groups of NPs and synthetic compounds, ensuring that the NP set we design enables to cover a sufficient chemical space that remains to be explored in the context of drug discovery.

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