What is molecular docking and its role in drug discovery?

Molecular docking in drug discovery

When we fall ill, doctors prescribe medications. Today, a plethora of medicines are available for various ailments in the market. However, behind every commercially available drug lies a lengthy journey, often concealed, involving the diligent efforts of numerous scientists, individuals, and industries.

The cornerstone of discovering these drugs is molecular docking, which plays a pivotal role. Presently, even before formulating a medicine, its effects and potential side effects can be ascertained without the need for extensive clinical trials. This advancement is attributed to molecular docking. Let's delve deeper into the concept of molecular docking.

What is molecular docking

What is molecular docking?

The term "docking" denotes the process of aligning or examining the interaction between any two molecules. Although the concept of molecular docking may appear intricate, let's understand it simply.

Consider a lock-and-key mechanism: every lock necessitates a specific key to open or close it. Using any other key renders it ineffective. Each lock features a unique shape within the hole for key insertion. A key is crafted to precisely fit this shape. Only when the key perfectly aligns with the lock's shape does it open. Similarly, molecular docking operates.

In every living organism, numerous enzymes govern cellular and bodily functions. These enzymes are proteins comprising amino acids. Each enzyme encompasses an active part responsible for a specific function. Enzymes possess distinct shapes, with up to 1000 amino acids in some cases. The arrangement of these amino acids creates particular cavities within enzymes. Only a specific molecule can fit into these cavities. For example, the enzyme amylase converts starch into maltose. Initially, the starch molecule fits into amylase's cavity before transforming into glucose. This cavity is referred to as the active site.

What is molecular docking

To comprehend these interactions, software is utilized to ascertain if any molecule fits into a protein's cavity. This process is termed molecular docking.

In molecular docking, the binding affinity of any molecule with a protein or enzyme is determined. Through various software applications, any molecule is docked within a protein to discern the part or active site of the protein where target molecule docks.

The molecule interacts with various amino acids in the active site of protein, involving hydrogen bonding and hydrophobic bonding. Software then computes a binding energy based on these interactions. The site where this binding energy is the lowest is typically a perfect docking site where our molecule can fit.

What is the role of molecular docking in drug discovery?

Drug discovery is a lengthy process, commencing with ideation and design. Researchers initially identify the specific enzyme they need to target for any disease. This concept is straightforward, as enzymes regulate body functions and cellular processes. So, if a particular enzyme is blocked, it won't be able to perform its related function. By altering the shape of a particular pocket or cavity, or deforming it, the enzyme can be inhibited.

How drug works via molecular docking?

After identifying the target, scientists design molecules based on existing commercial drugs, natural products, or their expertise. These molecules can either block the enzyme or fit into the specific pocket.

Every drug encompasses numerous functionalities, including aliphatic chains, aromatic rings, heterocyclic rings, and other elements like chlorine, nitrogen, fluorine, etc. Scientists may design approximately 1000 or more molecules, but only one may exhibit potential for commercial availability. Alternatively, none may show potential, or a promising molecule may fail in clinical trials.

Here molecular docking plays a crucial role in drug discovery by:

1. Screening out potential drug candidates: Molecular docking screens potential drugs from the designed ones.

2. Selecting specific functionalities and determining their positions: Molecular docking identifies which functionalities enhance the drug's effect and their optimal placement. For instance, positioning a chloro group at the para position of the phenyl ring in a drug can significantly enhance its efficacy.

3. In cost-saving: Molecular docking aids in identifying potent drugs, obviating the need to synthesize every molecule. This translates to substantial cost savings for industries and scientists.

4. In time-saving: Alongside cost savings, molecular docking also saves time.

What is role of molecular docking in drug discovery

In summary, molecular docking is a computer-aided technology for drug discovery. It facilitates the design of specific drugs, selection of functionalities, and their placement. Moreover, molecular docking not only saves money but also time. Owing to its pivotal role in drug discovery, the process has become considerably faster today.


I hold a doctorate in chemistry and have expertise in the intersection of organic and medicinal chemistry. My work primarily revolves around developing bioactive molecules with medicinal potential.

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