Protein Structure Similarity Clustering (PSSC)

‘Biology Oriented Synthesis’ (BIOS) refers to synthesize novel compounds with high biologically activity with the use of some ‘prevalidated’ structures. BIOS mainly contains the application of PSSC and scaffold trees methods. Scientists have utilized this method to offer new pathways to biologically predefined structures and corresponding target groups, helping to identify more potential hit compounds. The core assumption of PSSC technique is that structurally similar binding sites tend to bind structurally similar ligands. Thus, PSSC method can be applied to the design of target clusters and structural template libraries.

BOC Sciences has used PSSC method to address the structural diversity found in PSSC member protein binding sites and develop a NPs library based on scaffolds.

Natural Products: Biologically Validated Ligands

Most of NPs meet many of the prerequisites for biological relevance because of their ability to interact with a wide range of proteins. They have the following advantages that contribute to modulate protein functions:

• Synthesized and modified by a variety of proteins
• Scaffold with sufficient flexibility and rigidity
• Show a wide range of biological activities mediated by interactions with different proteins

Figure 1. PSSC guided focused library design. (Balamurugan, R.; et al. 2005)

PSSC-guided Natural Compound Library Design

The search for small molecules that regulate protein function plays an essential role in drug development. BOC Sciences has developed a novel strategy to rapidly and accurately identify these molecules. We have designed NPs libraries by using PSSC to explore the structural conservatism in protein domain area. Our method is described in detail as follows:

• Structural domains and proteins identified as being structurally similar in their ligand-sensing cores are grouped in a PSSC
• Since NPs can be considered as pre-validated ligands for multiple proteins, a NP that enables to interact with one of the PSSC member proteins is chosen as a guiding structure for compound library synthesis

Features of Natural Compound Libraries with the Use of PSSC

• Natural product libraries designed by using PSSC show ample chemical diversity
• This novel compound library design strategy provides a higher hit rate in small compound libraries of structurally similar proteins

BOC Sciences provides professional, rapid and high-quality services of Protein Structure Similarity Clustering (PSSC) at competitive prices for global customers. Personalized and customized services of Protein Structure Similarity Clustering (PSSC) 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!