Scaffolds and Scaffold-based Compound Library

Aiming to specifically target the binding sites, knowledge-based and diversity-based design elements are employed to design compound libraries. An important point of this method is to identify molecular building blocks or scaffolds that are compatible with binding sites, thereby capturing certain aspects of target specificity. In general, the selection of scaffolds are based on docking calculations and analysis of known inhibitors.

With extensive experience in organic synthesis and complex compound construction, BOC Sciences applies different strategies to enumerate various compounds from scaffolds or, alternatively, screen compound databases for molecules containing these scaffolds. Our experts have successfully completed various scaffold libraries for different HTS projects.

Application of Scaffolds and Scaffold-based Compound Library

• Provide one of the most comprehensive listings of privileged scaffolds
• Offer privileged scaffold library synthesis method in creative approaches
• Capture characteristic directionality in the presence of hydrogen bonds and aromatic interactions

Figure 1. 3D pharmacophores are generated with either structure- or ligand-based approaches. (Thomas, F.; et al. 2019)

Library Design Workflow

At BOC Sciences, chemically diverse building blocks for scaffold decoration are carefully designed and rigorously selected according to published criteria. Our groups apply lead-oriented synthesis principles to construct a high-quality Scaffolds and Scaffold-based Compound Library with optimal physicochemical properties.

• Firstly, we employ organic and analytical chemistry approaches (reaction-oriented scaffold design) to conduct scaffold selection and prioritization, where the chemical scaffolds are viewed as structural cores with several points of diversity
• Chemical modification is performed to generate different intermediates/building blocks
• We then carry out subsequent functionalization/decoration to provide the final compound
• Finally, retrosynthesis rules are utilized to isolate synthesis-relevant scaffolds from the compound set

Features of Scaffolds and Scaffold-based Compound Library

• BOC Sciences can provide customized Scaffolds and Scaffold-based Compound Library design services based on customer’s scaffolds or scaffold hopping in compliance with individual client’s requirements
• Be supplied with up to 200-500 compounds per scaffold
• Maximum structural diversity and rare chemotype selection
• Novelty for all scaffolds and potentially promising compounds verified by patent searches
• Similarity to molecules involved in the database
• The number of variation points per scaffold is kept in the range of 2-3, with preference given to structures with one variation point per cycle
• Several in-house structural physicochemical filters are applied
• Additional services of analysis and categorization by cheminformatics scaffold-based methods (based on 2D fingerprints, similarity or mathematical models) are available

What We Deliver

• Delivered within 2 weeks in any customer-preferred format
• Powders, dry films or DMSO solutions formatted in vials, 96 or 384-well plates
• All compounds have a minimum purity of 90% assessed by ¹H NMR
• Analytical data is provided

BOC Sciences provides professional, rapid and high-quality services of Scaffolds and Scaffold-based Compound Library design at competitive prices for global customers. Personalized and customized services of Scaffolds and Scaffold-based Compound Library design 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!