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Structure Based Drug Design Lab

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Medicilon has structure based drug design lab. Our structural biology department offers services supporting structure-based drug design from determination of novel targets to final structures. Our platform is one of the earliest established structural biology platforms in China and has been certified by the Shanghai Government.

Computational Biology & Molecular Modeling

  •     – Structural-Based Drug Design (SBDD)

  •     – De novo Drug Design 

  •     – Virtual Drug Screening

  •     – Quantitative Structure-Activity Relationship (QSAR)

  •     – ADMET Property Optimization


Fragment Based Drug Discovery (FBDD) Services

  1.     – In-house fragment library designed by medicinal chemists

  2.     – Construct focused library on  the target knowledge using molecular modeling

  3.     – Screen fragments mainly using X-ray technology

  4.     – Design novel scaffolds based on crystal structures

Structure-Based Drug Design (SBDD, also known as rational drug design) is a technique that accelerates the drug discovery process by utilizing structural information to improve the lead optimization process.  It has been estimated that SBDD can reduce the cost from target identification to investigational new drug (IND) filing by 50%. The technique requires a high-resolution 3D structure of the inhibitor bound to the target obtained using X-ray crystallography.  Once the structure is obtained, the interactions between the inhibitor and the active site of the target are analyzed. Improved inhibitors result from this analysis, resulting in a shortening of the lead optimization process.


A structure of a drug target can initiate and accelerate drug development in many important ways

I) The structure of the target by itself shows immediate novel opportunities for drug design
II) A structure of a target with a substrate or co-factor or TS Analog reveals which pockets can be filled by inhibitors and suggests which types of compounds to make
III) Structures of the target with low MW-low affinity “fragments” show where fragments bind and how to modify and/or link fragments – to achieve higher affinity
IV) The structure of a compound found in a screen in complex with the target reveals how the compound acts and how it can be modified for better affinity
V) Structures of successive compounds bound to the same target assist in understanding structure-activity relationships, binding modes and conformational
VI) The structure of a drug candidate in complex with the target can be helpful in devising strategies for modifications which MAINTAIN AFFINITY but improve e.g. drug bioavailability or decrease drug toxicity

VII) The structure of a drug: Target complex unravels the reasons for DRUG RESISTANCE

Structure-Based Drug Design Cycle

  • Target Identification and Validation

  • Assay Development

  • Virtual Screening (VS)

  • High Throughput Screening (HTS)

  • Quantitative Structure – Activity Relationship (QSAR) and Refinement of Compounds

  • Characterization of Prospective Drugs

  • Testing on Animals for Activity and Side Effects

  • Clinical Trials

  • FDA Approval

Our goal is to assist medical researchers with novel drug discovery and development. Pursuant to this goal we specialize in three primary tasks: lead discovery, lead optimization and x-ray crystallography.

Lead optimization is performed on compounds that have been discovered through computational and/or assay-based lead discovery. Two primary tools exist for lead optimization: RACHEL and CHARLIE, both SYBYL modules.

X-ray crystallography primarily consists of three stages: crystallization trials, data collection and structure determination & refinement. A successful x-ray crystallography run results in three-dimensional coordinates of a novel target protein that can be used for lead discovery and/or three-dimensional coordinates of lead compounds bound to validated targets to serve as a basis for lead optimization.

What We Can and Cannot Do


Small molecule conformation generation and energy profiling
Visualizing crystal structures
Binding site characterization
Virtual screening to enrich databases for actives

Cheminformatics, Ligand-Based and Structure-Based

Predict binding modes when receptor can be treated rigidly


Separating highly from weakly active compounds
Predicting side chain rearrangements and backbone relaxation

Very Challenging

Predicting binding free energies
Predicting large scale protein movements
Mapping free energy surfaces
Understanding off-target effects
Other ADME-Tox


Contact Us 

Email :
Tel : +86 021 58591500

Tips:  Above is part of Structure Based Drug Design Lab and structure based drug discovery. You can also CONTACT US with any question or enquiry you may have. We will be happy to discuss your needs in detail and design an appropriate plan of action.

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