Fragment-based Drug Design

Molecular docking is mainly used to determine the optimal position and orientation of small molecules in protein targets. Although the success of this method depends on the target and software, it is also associated with binding affinity. The quality of protein-ligand interaction can be expressed to some extent by ligand efficiency (LE), that is, the average binding energy of each ligand's non-hydrogen atom. However, most studies of molecular docking predictions favor molecular binding to protein targets with detectable affinity and usable crystal structure.

Process of drug designFigure 1. Process of drug design.

Our simulation services

Project name Fragment-based Drug Design
Samples requirement
  • Molecular weight < 300
  • clogP ≤ 3
  • Number of hydrogen bond donors ≤ 3
  • Number of hydrogen bond acceptors ≤ 3
Timeline Decide according to your needs.
Deliverables We provide you with raw data and calculation result analysis service.
Price Inquiry

Compared with the screening of large molecules, fragment screening has its practical advantages:

  • It is easier to collect, maintain, and screen a library of thousands of fragments than a database of millions of macromolecules, which allows companies and academic institutions to do lead discovery;
  • A higher screening hit rate can achieve complex targets, especially those involving protein-protein interactions;
  • In addition, the fragments are small in size and high in solubility, and usually have better drug properties. The structure of these fragments can be easily optimized at later development process. The potential to become drug molecules is also greater.

Advantages of Fragment-based Drug Design

Fragment-based Drug Design-1

Screening of fragment libraries

  • Ligand Observe NMR methods.
  • Saturation Transfer Difference (STD).
  • WaterLOGSY (wLOGSY).
  • Carr-Purcell-Meiboom-Gill (CPMG).

Library preparation of client or custom libraries

  • Identity, solubility, and purity determination.
  • Automated smart pooling.
  • Positive control at regular intervals.
  • Diversity analysis.

Follow-up analysis of hits

  • Validation (follow-up of singletons).
  • Rank-order; clustering of hits.

Target Protein Generation

  • Protein synthesis and purification.
  • Target Preparation.
  • Screen design.
  • Sample optimization.
  • Experimental optimization.

Applications of Fragment-based Drug Design

Our Fragment-based Drug Design including but not limit to:

  • Feasibility assessment of new drug targets.
  • High-throughput screening and active compound discovery based on structural design.
  • Discovery of active compounds to lead compounds.
  • Optimization of lead compounds to determination of preclinical drug candidates.
  • Research on structure-activity relationship.

Our advantage

  • Computer aided drug design save a lot of labor costs.
  • Short calculation period and fast speed.
  • The funds required are far less than biological or chemical experiments.
  • High calculation accuracy.

Related services

CD ComputaBio is a professional and efficient team. The team has more than 40% of employees with master degree, doctor degree and above. Treating customers' projects CD ComputaBio is racing against time, mission must be reached, efficient and timely delivery of tasks, customer satisfaction and trust. If you have drug design needs, please feel free to contact us!

* For Research Use Only.