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Computer Aided Drug Design


What Is Computer Aided Drug Design?

With the completion of the Human Genome Project, the rapid development of proteomics, and the discovery of a large number of genes related to human diseases, the number of target molecules have increased significantly. Computer-aided drug design driven by computer technology has achieved great progress in recent years. Computer-aided drug design is one of the most important methods for design of lead compound. Quantum mechanics, molecular dynamics, structure-activity relationships and other basic theoretical data are applied to study drug-efficacy models of the effects of drugs on enzymes, receptors, etc. The general process of computer-aided drug design is: Firstly, the structure of the receptor macromolecule binding site is obtained through physical techniques such as X-crystal diffraction technology, and then various molecular simulation methods are used to analyze the structural properties of the binding site, such as electrostatic field, hydrophobic field, and the distribution of hydrogen bond sites. Finally, the database is utilized to search or design new drug molecules, identifying molecules whose shape and physical and chemical properties match the receptor site, and these molecules are synthesized to test their biological activity. Novel lead compounds can be discovered after the above cycles in this way.

Computer assisted drug design pipeline.Figure 1. Computer assisted drug design pipeline. (Giulia, C.; Simone, B. 2017)

Our Computer Aided Drug Design Services

At Alfa Chemistry, we are capable of using a diversity of computational tools to support your Computer-aided drug design. Our teams can provide molecular docking simulation, molecular dynamics simulation, quantitative structure-activity relationships modeling and quantum mechanics.

Molecular docking

We provide molecular docking simulation to study the interactions between small molecules and their target protein or predict the binding affinity between them. We employ docking technique to dock drug candidates into macromolecules in which scoring binding affinity of two molecules or association to spatial orientation is applied to predict protein-ligand or protein-protein interaction when an agent is bound to a receptor (protein or enzyme). The main steps of docking simulation are as follows:

1) Accurate ligand insertion at the receptor binding site.
2) Estimation of the ligand affinity by a scoring function.

Molecular dynamics (MD) simulation

MD simulations provide comprehensive information on the conformational changes and fluctuations of nucleic acids and proteins, and have been widely applied in the investigation of complex processes that happened in biological systems such as conformational changes, protein folding, protein stability, molecular recognition and ion transport in biosystems. Our scientists apply this powerful tool to explore structural, dynamics thermodynamic, and energetic of biomolecules and their complexes based on molecular mechanics and/or the empirical force field (e.g. AMBER, CHARMM, GROMOS, and CVFF).

Quantitative structure-activity relationships (QSAR)

Only the knowledge of molecular structure is required for predicting desired property or activity in QSAR. We use the QSAR modeling to estimate the binding constant and thermodynamic stability. We are capable of developing 3D-QSAR models using comparative molecular field analysis region focusing (CoMFA-RF) and VolSurf methods. We can also build a QSAR model for predicting complexation by the topological substructural molecular design (TOPS-MODE) approach. At Alfa Chemistry, two different approaches are used to support QSPR modeling. One of them is based on descriptor approach using various geometrical, constitutional, electrostatic, topological, thermodynamic, and quantum chemical molecular descriptors. Another one is based on fragments method using different types of fragmental descriptors.

Quantum mechanics (QM)

We mainly apply semi-empirical processes: Density functional theory (DFT) and ab initio methods to calculate the binding free energy. Different QM methods (e.g. PM6, HF, ONIOM) are applied to examine the structures. Alfa Chemistry provides accessible and well-characterized force field to accurately depict the geometries or energetics of intermolecular interactions.

Application of Computer Aided Drug Design

Active site analysis

The information about receptor binding obtained from active site analysis is useful in the guidance of designing new drugs. We perform active site analysis using various software including DRID, GREEN, HSITE, etc. In addition, there are some software based on Monte Carlo and simulated annealing technology such as MCSS, HINT, BUCKETS, etc. The active site analysis process is as follows:

1) The dynamic method is used to search for the binding area of molecular fragments and receptors.
2) 100-1000 copies of each fragment are selected, and energy optimization is performed in the binding domain of low-energy fragments.
3) In the final energy search process, random sampling or grid points can be used to implement.

Database search

Database search methods can be divided into two categories. One is based on ligands, that is, searching the three-dimensional structure database based on the pharmacophore model. Another type of method is receptor-based, also known as molecular docking. We use the potential energy function of the molecular force field as the evaluation function, and introduce scoring function optimization and chemical property matching for molecular docking. In addition, we have also established another fast and accurate flexible docking algorithm, which considers many conformations of the ligand molecule during docking. This method can be used for medium-scale 3D database search with the application of the empirical binding free energy function for evaluation.

Alfa Chemistry's Advantages

Our groups have delivered multiple computational tools in an integrated Computer-aided drug design platform.

  • Eliminate the demands of managing infrastructure and orchestrating calculations
  • Integrate third-party or in-house tools
  • Control costs by fine-tuning when and how your calculations run
  • Leverage pre-built workflows or customize your own

Our Computer Aided Drug Design services remarkably reduce the cost, promote further experiments, and accelerate the process of drug design for customers worldwide. Our personalized and all-around services will satisfy your innovative study demands. If you are interested in our services, please don't hesitate to contact us. We are glad to cooperate with you and witness your success!


  • Giulia, C.; Simone, B. Breakthroughs in Computational Approaches for Drug Discovery. Journal of Drug Research and Development. 2017, 3(1).

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