3D-shaped Fragment Library

Molecular shape is one of the key factors in biomolecular recognition and its affinity to the binding site. However, most of the existing drugs have centered in the sp²-rich aromatic core. In addition, the same core moiety can usually be found in several drugs with different targeted diseases, which can directly result in low specificity or selectivity and side effects. Although most fragment libraries provide a high degree of diversity and have been improved to include the proper balance of attributes, they all tend to have a limited shape diversity. Nowadays, the synthesis of chemical fragments with 3D shapes is one of the current trends, especially for biological targets, such as the tough sp³ carbon for protein-protein interactions, which can increase the number and scope of fragment growth vectors. It is proved that a higher 3D of the molecule is an ideal feature of the candidate drug. At BOC Sciences, 3D features are usually added in the fragment optimization stage, and even fragments lacking a chiral center may adopt a 3D or chiral conformation when binding to a protein target.

Figure 1. 3D-Fragment-Consortium Fragment Library. (Pearce, N.; et al. 2016)

Advantages of 3D-shaped Fragment Library

• The use of more complex and more 3D-like sp³-rich fragments can create a broader chemical space of drug-like fragments
• Facilitate the exploration of more demanding biological targets

3D-shaped Fragment Library Characteristics

At BOC Sciences, we have designed a 3D-shaped Fragment Library using various physicochemical properties and descriptors, which can evaluate the 3D dimension and diversity of molecules. Our 3D-shaped Fragment Library contains more than 3,000 fragments, which is a reliable source of high-quality fragments. We cooperate with leading experts in the field of FBDD to design and supply top-level fragment libraries, aiming to meet different requirement of each client.

Table1. The summary of the BOC Sciences 3D-shaped Fragment Library characteristics

Features of 3D-shaped Fragment Library

• The Rule of Three with multiple filtering criteria are applied to BOC Sciences General Fragment Library
• The Principal moments of inertia (PMI) calculation is used for calculating and evaluating 3D-dimensionality
• The appropriate diversity level of the library is proved by applying the maximum Tanimoto coefficient of diversity 85% (using linear fingerprints)
• The 3D Fragment Library covers a diversity of molecular shapes: rod-shaped, disc-shaped and spherical with sufficient diversity
• The undesirable function is eliminated by applying PAINS and our unique in-house medicinal chemical filters
• All compounds can be used for cherry-picking

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 3D-shaped Fragment Library design at competitive prices for global customers. Personalized and customized services of 3D-shaped Fragment 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!