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Virtual Screening

Updated: Apr 1, 2021

Virtual screening (VS) or in silico screening refers to the process of identifying new possible drug candidates using computational techniques to analyze large chemical databases. Virtual screening is used to evaluate large libraries of various compounds (ligands) via computational tools. Virtual Screening approach is based on the laws of quantum and molecular physics.

The main principle behind this approach is to measure the presence or absence of particular structures and substructures, matching particular calculated molecular properties, and fitting putative ligand molecules to the respective active site of the biological receptor. In this way, using this approach, we can design and optimize different libraries from the available compounds. Due to decreased cost and increased accuracy of this approach, this method has become an indispensable part of computer-based drug discovery and designing.

This approach uses computer programs and tools to search the chemical libraries stored in the chemical databases. It is an automated process as the computer screens through the huge number of the compounds in order to search for the suitable compounds for the drug discovery, the small constituents the computer tries to identify which are likely to bind suitably to the drug target that may be a protein receptor or a specific enzyme. Virtual screening is often used when the ligand number is expected to be >10,000.

Types of Virtual Screening

There are two notable methods used in Virtual Screening:

1. Structured-based - involves the application of the scoring functions to the docking of the candidate ligands compounds with the target protein molecule. This is carried out by checking the binding affinities of the ligand to a high-affinity protein molecule.

2. Ligand-based - depends on the knowledge of other molecules that bind to the biological target of interest and the structure of the ligand is not known. These other molecules are utilized to derive pharmacophore models (Pharmacophore modeling) or alternatively Quantitative-Structure Activity Relationship (QSAR).

Steps Involved in Virtual Screening

The process of virtual screening has mainly the following steps involved:

1. Screening Library - requires a chemical library of the compounds that store the small constituent molecules for the drugs which are considered as the suitable hit or the chemical compound that is considered biologically appropriate for the development of the drug. The library consists of a tremendous amount of the chemical compounds that are stored in the databases. The database consists of suitable information about the compounds it contains which are:

  • Purity

  • Structure

  • Physicochemical properties and quantity of the compound

2. Similarity Search - involves the finding of the proper compounds that have structural similarity to the biologically active compounds which also have a probability of being active. The process involves various methods to found the active molecules.

3. Pharmacophore - involves the characterization of the compounds to carry out the identification of hit, lead optimization and rationally designing a new drug. The pharmacophore model represents the set of features of the chemical compounds that are common to the series of biologically active molecules for drug discovery. These features are mainly represented as the functional groups and are termed as Pharmacophoric groups, which are as follows:

  • Hydrogen-Bond donors and acceptors

  • Positively and Negatively charged groups

  • Hydrophobic regions

4. Docking - involves the prediction of the proper orientation of the molecule that fits into another molecule to form a stable adduct molecule. Mostly, the docking is used in drug designing to predict the fitting of ligands with the enzyme molecule. The basic purpose of the docking is to reveal how the ligands interact with the target molecule and to predict the binding strength and predict the signal they produce.

5. Cherry Picking - the most crucial step for drug designing - involves the picking of the suitable compounds or the lead molecules’ identification. The selection criteria are based on the filtered molecular data from the small molecular collection that was screened. The purpose is to pick the most suitable molecules that can prove in the potential drug discovery.

Importance of Virtual Screening in Drug Designing

Virtual screening for the identification of lead compounds in the process of drug designing plays an essential role. In comparison to the laboratory experiments, VS is a cost effect method for lead identification and investigates the compounds that have not yet been synthesized. Virtual screening can be used to reduce the initial number of compounds before using expensive high-throughput screening methods.

Databases for Virtual Screening

There are various databases available for screening a compound virtually. These include:

  • GDB-17

  • PubChem

  • ChemSpider

  • ZINC

  • ChemMine

  • ChEMBL

  • ChemBank

  • BindingDB

  • Drug Bank

  • KEGG Ligand

Bioinfolytics & Our Services

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