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Ligand Based Drug Design

Paper Type: Free Essay Subject: Biology
Wordcount: 1108 words Published: 29th May 2018

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In practice, drugs were found by synthesizing the variety of compounds in taking a long time as well as many step processes against in vivo biological screens and additional examine is required for their pharmacokinetic properties, metabolic studies and possible toxicity studies. Such pre determined development process has resulted in higher success rates. This type of systematic development process which reduces the various failures such as poor pharmacokinetic studies, lack of efficacy, animal toxicity, adverse effects in humans and various miscellaneous factors.

The process of drug discovery has been a cause of major changes with the arrival of genomics, bioinformatics, proteomics, and effective technologies like, combinatorial chemistry, virtual screening, high throughput screening (HTS), de novo drug design, in vitro studies and in silico studies for pharmacokinetic screening and also for the structure-based drug design.

The In silico procedures are very useful in identifying drug targets via bioinformatics tools such as computer software programs. Further it is used to examine the lead structures for potential binding or active sites, produce structurally similar molecules, verifying for its drug likeness properties, dock these active molecules (ligands) with the target enzyme, arrange them according to their binding attractions, and finally optimize the lead molecules for to enhance its binding properties.

Nowadays the computers and various computational methods are developed for following reasons such as,

  • To reduce the complexity
  • Time consuming
  • Accurate results
  • Reproducibility
  • Lower cost
  • Novel target identification

Various facilities which brings the drug discovery process in a very simplest way those are,

  • High performance computing
  • Data management software
  • Internet and etc.,

Major advantages of computation in the drug development process as follows,

  • Virtual screening and de novo drug design
  • In silico pharmaco kinetic properties prediction
  • Improved methods for to determine protein-ligand binding.

Currently various protein targets are available through many newer techniques such as

  • Crystallography
  • NMR
  • Bio informatic methods,

Nowadays the demand is increased for computational methods that can encounter and examine active sites of the lead molecules and propose its possible drug molecules that can bind particularly in these binding sites. Usage of computers at early steps is concurrently reducing the cost and time need for the drug discovery and development process.



It depends on the wisdom of three-dimensional structure of the protein molecule. Practically the structure was initially identified by X-ray crystallography which improves the aptitude to produce new drugs that fight against diseases. The awareness of the three-dimensional protein structure is required for the design of a new compound. Commonly new compound is arranged atom by atom become optimal and the important properties like shape and charge which perfects with the active site of the particular protein target to increase their interaction and block the protein function automatically. (Fig. 1 demonstrates the structural similarity between the lead molecule and the target enzyme’s active site).

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The lead molecule has been synthesized after that X-ray crystallography is used to examine the structure of target protein bound to the unknown lead molecule. (Fig. 2 illustrates the binary complex of a lead molecule bound to the target enzyme’s active site). The binary complex exhibits how the molecule tie with the active site of the given target protein. By obtaining this structural knowledge, lead molecules are redesigned, synthesized, refined and finally examined in a proper way until to get adequately potent drug has been intended and optimized for the desired action.


It is otherwise known as indirect drug design. It trusts on the awareness of different new ligand molecules that bind with the target protein molecule. These different designed molecules are used to develop a new strategy which explains the each and every individual element responsible for the interaction between ligand and target protein molecule. (Fig. 3 provides the information about all the ligand features important for target protein interaction, for ex: H-bond acceptor region).

Inclusion of these elements into a ligand should enhance the ligand – protein interaction. Moreover a target protein model is produced based on the composite ligand.

Ligand based drug design is depends on the information of other molecules which bind to the biological target active site with their interest. These types of molecules are used to extract a suitable model which provides the important structural properties of a lead molecule which helps in the binding process with the target molecule.

Biologically active target model is designed based on the information of binding molecules. This model is used to develop novel compounds which interact with the biologically active target molecule.

Quantitative structure activity relationship is defined that a correlation between calculated properties of the molecules and it’s experimentally determined biological activity was derived. QSAR studies are used to predict the activity of the new molecules.

Normally protein model is designed for to get more and more information about the various ligands and its interaction with the target protein. The important target for the rational drug design is protein molecule should act as an enzyme. Enzymes are the molecules which catalyze the biochemical reactions by reducing the energy level from the substrate molecule into product formation. But, malfunctioning enzyme causes the disease.

The prime aim of rational drug design is to generate an extremely active and selective compound that should bind only to the active site of malfunctioning enzyme. And further it prevents the defective enzyme’s function and simultaneously inhibits the progression of the disease.


In the Drug design process, from the target identification till the drug confirmation various steps are involved. These steps produce the geometrical development of a novel drug. Those steps are as follows,


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