Fragment based drug discovery

Your way to drugs for challenging targets

 

Learn more2bind Services for FBDD

 Why fragment-based drug discovery (FBDD) ?

Challenging drug targets require smart solutions off from the beaten path of compound-based drug discovery.

Fragment-based drug discovery (FBDD) reduces the molecular size of the chemical compounds (thus “fragments”) and by that drastically increases the chemical space that can be sampled.

Due to their higher “simplicity” such chemical fragments have higher chances of interacting with binding groves and pockets of proteins. In a sense, they only provide the minimal binding surface required for an interaction. State-of-the-art fragment libraries cover large portions of chemical space and thus high hit rates are often obtained. From an initial fragment, chemical optimization and “fragment growth” lead to more complex and better-adapted chemical structures.

Of course, the smaller fragments often display weaker binding than larger and more complex chemical compounds. However, with the right tools at hand, such weak binding can be reliably and efficiently be detected.

Our specialized MST and nanoDSF fragment-based drug discovery services are tailored for the detection of fragment binding.

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High diversity

Due to their small size, chemical fragments can be generated with vastly different chemical properties.

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High hit-rates

“Simple” chemical fragments can lead the way to binding into complex binding pockets and groves.

Efficient libraries

Fragment libraries are usually small (1000-2000 entities) and highly diverse at the same time, thus saving costs.

Optimizable

Chemical fragments can be linked and modified (“fragment growth”) to yield more complex chemical structures.

An optimal fragment library

> Highly soluble fragments to cope for weak binding affinity (usually µM to mM)

> Molecular weight of fragments around 300 Da

> Less than three H-bond donors/acceptors per fragment

> Less than three rotatable bonds

> High hydrophilicity (water solubility; cLogP less than or equal to 3)

Be assured. We have the right fragments!

> Choose our specialized, high diversity library of ~2000 fragments

Benefit from our connections for sourcing any fragment library available

> Use your own and trusted fragment libraries

2bind fragment-based drug discovery services

Efficient fragment screening often requires high fragment concentrations due to their weak base affinity. This results in high DMSO or solvent contents in an assay. Thus, assays providing the required throughput and necessary robustness in high solvent settings are needed. 

In order to fulfill these requirements, 2bind thus offers fragment-based drug discovery by utilizing two true biophysical methods:
MicroScale Thermophoresis (MST) and nano-Differential Scanning Fluorimetry (nanoDSF). Both methods allow high throughput, high fragment concentrations, and high solvent contents.

We combine these methods with state-of-the-art liquid handling and dispensing setups, such as the LabCyte Echo system and liquid handling robot platforms. This means there is no need for any liquid handling or preparation of fragment solutions on your end.

You can choose whether you want to work with our library of ~2000 fragments or utilize your own fragment collection.

MST fragment screening

  • Automated fragment screening based on the MicroScale Thermophoresis principle.
  • Minimal sample consumption
    (low nM concentrations and µL volumes).
  • Single-dose and full dose-response assays.

Echo 550 Acoustic Liquid Dispensing

  • Contact-less, precise nL volume transfer for preparation of fragment dilution series.
  • Highest throughput and lowest plate preparation time.

nanoDSF fragment screening

  • Fragment screening based on shifts in thermal stability of a target upon fragment binding.
  • Minimal samples consumption (low µM protein concentrations and µL volums).
  • Single-dose and full dose-response assays.

 

MST-based fragment screening

2bind´s MicroScale Thermophoresis (MST) based fragment screening services are characterized by fast turn-around times and attractive cost structures. MST tells – among other parameters – the steady-state binding affinity for each fragment in solution.

Besides affinity values, important additional information on unspecific adhesion of fragments on surfaces or fragment-induced target aggregation or precipitation are obtained.

The method works extremely well at high fragment concentrations (up to 10 mM assay concentration). It consumes very little amount of the target (typical a few µg of protein, mostly even less of RNA and DNA).

2bind is the first contract research organization certified for the use of MST by NanoTemper Technologies.

nanoDSF-based fragment screening

2bind’s nanoDSF-based fragment screening offers rapid qualitative information on whether fragments are binding to a target protein or not.

Measurements are performed without any modification of the target protein in solution. For this, the intrinsic tryptophan fluorescence of the target protein is used to record its thermal stability. Possible changes of protein stability by fragment binding (stabilization and destabilization) are thus evident.

The method works extremely well at high fragment concentrations (up to 10 mM assay concentration). It consumes very little amount of the target (µg amounts of protein).

2bind is the first contract research organization certified for the use of nanoDSF by NanoTemper Technologies.

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