Compound Docking

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Compound Docking

Compound docking is an important method in drug virtual screening, and it should be improved by applying in the study of interaction between immobilized ligand and protein. Several groups have used homology models to design or discover ligands for target proteins. And the success of a docking screen can be evaluated by its capacity to enrich the small number of known active compounds in the top ranks of a screen from among a much greater number of decoy molecules in the database. The structure-based screening through docking is mature enough to be considered as a first-line technique in pharmaceutical discovery research.

Application of Compound Docking

Docking has been used to discover novel ligands for well over 30 targets and work has continued to focus on enzymes. The inhibitors discovered were novel, having little similarity to the known ligands. Most initial leads had affinities in the low-micromolar range. The new sulfonamide inhibitors of carbonic anhydrase II are the exception - they are much more potent, but not completely novel. There has been an efflorescence of new docking methods in the past several years, and several docking programs were used in these studies. The compound docking screens of chemical databases are widely used for ligand discovery. And the docking predictions captured the X-ray results well. Besides, docking can suggest new ligands and also their bound geometries with some accuracy. Docking against homology-modeled structures has also been used to improve the pharmacokinetic properties of known inhibitors and to develop or expand structure–activity relationships. Some docking methods have been used with modeled structures to develop new inhibitors.

Our Services

Detailed preparatory work to model the protein active site

We need to do a lot of modeling work to establish the relationship between human target proteins and distant relative proteins in the literature. We have established sequence alignment and comparison to enable us to build three-dimensional models of the goal and its interaction with ligands.

We have a good model of the protein-ligand system. The next step is to remove the ligand and docking. Docking is first tested on molecules known to bind to the target. This leads to excellent retrieval rates, indicating that the model will also be able to retrieve new compounds.

A large number of compounds were analyzed in detail. We visualized each compound and observed each docking position. Docking provides a good geometric structure for ligands, and we use Cresset software to check whether electrostatics makes sense. Any compound that can't bind well is rejected.

Why Choose BOC Sciences?

BOC Sciences has a large group of experts in the computational chemistry who specialize in molecular modeling and compound docking. They are proficient in various search algorithms and combine information from different scoring functions to balance errors in single scores and to improve the probability of identifying “true” ligands. There is no doubt that our compound docking service will play a very critical role in promoting your drug discovery process.

References:

  1. Schneider, G., & Böhm, H. J. (2002). Virtual screening and fast automated docking methods. Drug discovery today, 7, 64-70.
  2. Shoichet, B. K., McGovern, S. L., Wei, B., & Irwin, J. J. (2002). Lead discovery using molecular docking. Current opinion in chemical biology, 6(4), 439-446.
  3. Ewing, T. J., & Kuntz, I. D. (1997). Critical evaluation of search algorithms for automated molecular docking and database screening. Journal of Computational Chemistry, 18(9), 1175-1189.
  4. Fukunishi, Y., Mikami, Y., Takedomi, K., Yamanouchi, M., Shima, H., & Nakamura, H. (2006). Classification of Chemical Compounds by Protein-Compound Docking for Use in Designing a Focused Library. Journal of medicinal chemistry, 49(2), 523-533.
  5. Huang, N., Shoichet, B. K., & Irwin, J. J. (2006). Benchmarking sets for molecular docking. Journal of medicinal chemistry, 49(23), 6789-6801.
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