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Target Fishing


Target fishing is an essential step in modern drug development to explore the mechanism of action of bioactive small molecules by identifying their interacting proteins. Various computational target fishing methods are designed to identify the most promising target of a query molecule. The llarge amount of information regarding the bioactivity of thousands of small molecules now allows the development of these types of methods. In recent years, a diversity of computational target fishing technologies have been developed to efficiently and effectively screen for targets in a high-throughput format, which is expected to have a large impact on drug development.

Application of Target Fishing

  • Prediction of the bioactivity of a compound
  • Identification of the mode of action of known drugs
  • Detection of drug polypharmacology
  • Drug repositionin
  • Prediction of the adverse effects of a compound

Overview of the main target fishing approaches.Figure 1. Overview of the main target fishing approaches. (Salvatore, G.; et al. 2021)

Our Target Fishing Methods

At Alfa Chemistry, we focus on two types of in silico target fishing strategies which are ligand-based and receptor-based approaches:

1. Ligand-based approaches

Ligand-based approach is a type of standard target fishing strategy which is widely because they can be used when the protein structure data is unavailable and are easy to conduct.

  • 2D-structure similarity searching

We perform it by ranking the matched molecules according to their similarity index with respect to the query compound, and the top molecules are selected for the final prediction.

  • Mixed 2D/3D-structure similarity searching

Alfa Chemistry combines 2D and 3D similarity to provide a target score obtained by a cross-validation analysis method. The results obtained by this approach can be used to explore new scaffold models. Moreover, we provide a web tool with a client friendly graphical interface to perform reverse screenings by employing a well-prepared and ready-to-use chemical library.

  • Data mining and machine learning

One of the main challenges of computational target fishing methods is to determine the biological results of the combination of search molecules and their predicted targets. Therefore, we have developed data mining and machine learning-based methods, also known as chemical genomics methods which usually combine fingerprints and certain types of machine learning methods, to develop predictive models. Alfa Chemistry supports random forest (RF), naive Bayesian (NB) and support vector machine (SVM) methods and we also provide classical quantitative structure-activity relationships (QSAR), proteochemometrics-based (PCM) strategies, and model-stacking approaches.

2. Receptor-based approaches

We mainly apply protein structural information to predict ligand-target pairs. Our receptor-based approaches can be used to not only predict the potential off-targets of small molecules, but also their putative binding modes within the receptors. We use this strategy to study their mode of action and rationally design selective compounds.

  • Molecular docking

We apply molecular docking to predict noncovalent binding of macromolecules or a macromolecule (receptor) and a small molecule (ligand) efficiently.

  • Reverse docking

Our groups apply this powerful tool to identify potential protein targets for a given small-molecule ligand among a large number of protein targets. Our reverse docking contains the following steps: generation of a target structure database, prediction of energetically favorable binding conformations of the query ligand within the different targets, and ranking according to their docking score.

  • Pharmacophore mapping approach

Our scientists apply it to find the best mapping poses of the query molecule against all the pharmacophore models and list the top N best-fitted hits with appropriate target annotations, as well as the aligned poses of the respective molecules.

  • Targets checked by the chemical-protein interactome (CPI)

For each chemical-protein pocket pair, CPI refers to the interaction information of a panel of chemicals across a panel of target proteins in terms of binding strength and binding conformation. At Alfa Chemistry, we apply CPI to identify potential target.

Our target fishing 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!


  • Salvatore, G.; et al. Recent Advances in In Silico Target Fishing. Molecules. 2021, 26(17): 5124.

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