Structure-based Drug Design

A large number of successful cases proved that structure-based drug design (SBDD) technology plays an important role in the progress of drug research. Creative Biolabs is a world-leading service provider. Based on our powerful technology, we are fully committed to providing high-quality and low-cost services to advance drug research.

The development of drugs has always been recognized as a time-consuming and laborious task because the process involves knowledge of many different disciplines. A variety of drug design methods will be beneficial to the design and search for reasonable drug molecules, thereby speeding up the entire drug discovery process. In the past few years, advanced science and technology have accelerated the identification of three-dimensional protein structures, and genetic information has become easier to obtain. Therefore, SBDD has gradually emerged as an effective tool to help researchers predict the position of small molecules in the three-dimensional representation of protein structures. The important thing is that they also speed up the discovery of drugs, greatly reducing the time and cost of drug research.

Introduction of SBDD

Structure-based drugs rely on available structural models of the target protein. These models can be provided by methods including X-ray diffraction or molecular simulation. SBDD is mainly divided into several steps including protein structure preparation, binding site identification, ligand library preparation, docking, and scoring functions. Generally speaking, after capturing the structure of receptor macromolecules, molecular modeling software can be used to analyze the physical and chemical properties of the drug binding site on the receptor. Then, search the small molecule database to find the target molecule. These molecules are then synthesized, and they will be tested for further drug development.

Outline of SBDD. Fig.1 Outline of SBDD. (Ferreira, 2015)

Applications of SBDD

There are plenty of methods used in the early stages of drug discovery. Among the numerous methods, SBDD is one of the most powerful strategies. This method integrates traditional and modern technologies in the fields of medicinal chemistry, computational chemistry, biochemistry, and structural biology. The development of medicinal chemistry has led to an increasing number of successful applications of structure-based methods. Some successful examples include inhibitors of neuraminidase, renin, tyrosine phosphatase, β-lactamase, carbonic anhydrase, and DNA gyrase. In summary, this method greatly facilitates drug discovery.

Progress and Advantages

With more biological molecule’s 3D structures being identified through experimental or computational methods, SBDD approaches, which are time-saving, cost-effective and productive, have been widely used to design and discover novel lead compounds for associated diseases targets. The rapid development of SBDD is a key enabler to promote fragment-based drug design (FBDD). FBDD plays a key role in more than 30 clinical drug candidates and three oncology drugs. The main principle of FBDD is to use a small library of compounds to efficiently sample the chemical space, which makes it a supplementary method for high-throughput screening of large compound libraries. Currently, FBDD is widely favored by major pharmaceutical companies.

Creative Biolabs has established many high-standard structure-based drug discovery and screening platforms and successfully provided technical support for the development of multiple drugs. If you are interested in our SBDD related services, please feel free to contact us.

Reference

  1. Ferreira, L. G.; et al. Molecular docking and structure-based drug design strategies. Molecules. 2015, 20(7): 13384-13421.
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