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Hit Identification


Hit identification is a powerful tool for discovering compounds with the desired activity against a fully validated target. Hit identification is an essential step of the drug discovery process, in which the identified small molecules will bind to the target, usually a protein. Scientists therefore can modify its function and improve bioactivity. Identifying the right hit is the key in research as it reduces the attrition rate. Depending on the nature of the project, Alfa Chemistry’s team applies the most appropriate hit identifying approach to successfully identify a hit series that are validated having the best chance of developing into drug-like compounds.

From hit identification to lead optimization and candidate selection.Figure 1. From hit identification to lead optimization and candidate selection. (Salum, L. B.; Andricopulo, A.D. 2009)

Our Hit Identification Approaches

In order to identify high-quality durable hit series, Alfa Chemistry chooses the following mentioned hit identifying approaches either individually or in parallel, depending on the nature of your project.

  • Structure-based virtual screening

Our teams can analyze structural information about your nominated target, and design prospective ligands. We can also identify any differences which may enable the design of selective compounds by overlaying the target on related protein structures. Our structure-based virtual screening methods are as follows:

1. Molecular docking of 3D databases into a given target protein.

2. Rescore the hits using Implicit solvation binding energy (MMGBSA).

3. Identify the hits based on the binding energy and hotspot interaction patterns by employing machine learning tools.

4. Further evaluation of identified hits for various target-based properties including solubility, toxic groups, TPSA.

5. Study the stability and interaction modes using molecular dynamic simulations.

  • Ligand-based virtual screening

We perform ligand-based virtual screening for hit identification when the three-dimensional structure of the target is unknown, and we are committed to providing the following services:

1. Cluster analysis and identify a subset of molecules for further development.

2. Quantitative structure-activity relationship (QSAR) modeling with data curation methods and machine learning algorithms.

3. Further explore SARs around chemotypes of dataset.

  • Pharmacophore-based screening

Our groups conduct pharmacophore study on a series of known active compounds utilizing conformational analysis, molecular superposition and other methods.

1. Identify the common features of a series of known active compounds.

2. Screen the databases and identify the hits which are geometrically fitting to the features of the pharmacophore.

  • Shape-based screening

At Alfa Chemistry, we perform shape-based screening to identify new compounds with shapes that are similar to the known binder using the structure and shape of a compound known to bind to a target.

  • Similarity-based screening

We perform similarity searching using multiple molecular descriptors such as physicochemical properties, 2D properties, and 3D properties.

  • Fragment-based drug design

In fragment-based drug design, our experts dock the fragment libraries as probes in the binding site to scan suitable molecular fragments that bind in specific pockets. And the molecular fragments with a linker is able to be transformed into a new hit.

Features of Our Hit Identification

  • High-quality in silico screening
  • Capable of identifying multiple targets
  • Accurate computational calculations

Alfa Chemistry's Advantages

  • At Alfa Chemistry, hit series with the best properties for progression are identified through the careful and experienced integration of different screens and filters.
  • Our computational screening techniques can be carried out in parallel with HTS and/or fragment campaigns to capture both focused and diversity approaches to hit identification.
  • A diversity of computational calculations are applied to identify chemical compounds with an enhanced probability of acting on the target of interest with the desired biological effect.

Our hit identification services remarkably reduce the cost, promote further experiments, and accelerate the process of drug design for customers worldwide. Our personalized and all-around services will satisfy your innovative study demands. If you are interested in our services, please don't hesitate to contact us. We are glad to cooperate with you and witness your success!


  • Salum, L. B.; Andricopulo, A.D. Fragment-based QSAR: perspectives in drug design. Molecular Diversity. 2009, 13(3): 277-285.

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