Bioinformatics Computational Biology System Biology

Prediction of BioActive Molecules

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The prediction of biological targets of bioactive molecules from machine-readable materials can be normally performed by computational target prediction tools (CTPTs). However, the prediction of biological targets of bioactive molecules from non-digital materials has not been possible due to the complex nature of bioactive molecules and impossibility of employing computations. It was very important to predict the targets with accuracy and are the most important challenge for computational target prediction. A minimum structure is identified for each group of neighbor molecules in the proposed method. Each group of neighbor molecules shows a distinct structural class of molecules with the same function in relation to the target. The minimum structure is usually used as a query to search for molecules that perfectly satisfy the minimum structure of what is guessed crucial for the targeted activity. 

The known target of the neighbor molecule is used as a reference for predicting the target of the neighbor molecule with an unknown target. A lot of information is needed to identify the minimum structure, because it is necessary to know which parts of the bioactive molecule determines the precise target or targets responsible for the observed phenotype. 

Since only molecules that perfectly satisfy the minimum structure are considered, the minimum structure can be used without similarity calculations in non-digital materials and with similarity calculations in machine readable materials. 

Tools 

  • PASS online
  • PPB
  • SEA
  • TargetHunter
  • PharmMapper
  • ChemProt
  • HitPick
  • SuperPred
  • SPiDER

Target-identification and mechanism-of-action studies have important roles in bioactive molecule probe and drug and pesticide discovery. Experimental and computational approaches are used to predict biological targets that interact with bioactive molecules. 

Common Drawbacks 

  • Experimental approaches are usually more costly and slower than computational approaches
  • Computational approaches make predictions based on models with several approximations
  • The real predictability beyond training space cannot always be guaranteed 

Computational approaches can facilitate the study of biological targets of bioactive molecules and help the discovery of on-target and off-target effects and understand the mechanism of action of bioactive molecules, thereby playing a crucial role in many scientific projects. 

Working

The query molecule is used to search for structurally related bioactive molecules with similar chemical scaffold and similar substructures. 

Data Collection

The target information is collected for all structurally related bioactive molecules. If the target of the query molecule is not known, information on the structure activity relationship and the pharmacophore will be collected for all structurally related bioactive molecules. If the target of the query molecule is known, information on the structure activity relationship and the pharmacophore will be collected only for structurally related bioactive molecules with the same target as the query molecule. 

Minimum Structure Identification

A minimum structure does not represent a real molecule or a real association of functional groups, but is a part of a molecular structure that is necessary to ensure the target prediction of bioactive molecules. The minimum structure describes the presence or absence of chemical features in the molecule. It can be employed for distinguishing bioactive molecules based on their targets without similarity calculations in non-digital materials and with similarity calculations in machine-readable materials. 

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