HitGen have established a comprehensive team to run drug discovery projects using structure-based drug design technology. Our capability includes crystal structure generation, homology model generation, molecular docking and modelling, as well as an expert computational team.
We can leverage crystal structures, when available to predict and optimize the position of small molecules within a three-dimensional representation of the protein structure and estimate the affinity of ligands to target protein.
In the absence of X-ray crystallography data, we have extensive experience in construction and optimization of homology models based on related proteins.
Lead optimization is applied for screening a congeneric series of molecules. Conformations of R-groups are sampled and optimized, increasing the likelihood of identifying the correct binding mode.
Fragment-based drug design is supplied as a complementary approach of SBDD. Although fragments typically bind with a low potency, they form efficient interactions with the protein target and thus provide attractive starting points for compound design.
Target flexibility in molecular docking should be accounted throughout the modeling phase. We in addition provide induced-fit docking and molecule dynamic simulation strategies to obtain diversified protein conformation and handle the flexibility issues of crystal structures.
Solvation effect during docking progress also can be considered especially important for highly solvated ligands. We can effectively combines the solute energy and solvation energy in the optimization of binding affinity and high capability to identify the "native" binding conformation among the decoys.