Fluorine Fragment Library

It was demonstrated that ¹⁹F NMR-based fragment high throughput screening could be used as a very efficient tool for rapid and sensitive detection of fragment hits in FBDD [1]. As shown, although the fraction of chemical space covered by fluorine-labeled fragments may be limited compared to that covered by non-fluorinated fragments, similar hit rates are obtained applying both methods. At the same time, fragment screening with a simple one-dimensional ¹⁹F NMR experiment (with ¹H decoupling) is significantly faster and, in many ways, more robust than traditional ¹H-based NMR screening.

An in-house developed method focuses on the use of a fluorine nucleus as a detection tool. After a ¹⁹F fragment screen, protonated analogs of hit compounds can be mined and pursued in initial hit expansion. This approach can significantly add to the chemical space explored and also provide valuable information and early-stage SAR to chemists.

The Life Chemicals Fluorine Fragment comprises more than 5,400 fluorine-containing fragments from the General Fragments Stock Collection. The Advanced Subset of nearly 1,800 drug-like fluorinated compounds was selected by the following physicochemical criteria: 

Parameter

Range

MW

≤ 300

ClogP

 3

Fsp³

> 0.4

Number of rings

1 - 3

Rotatable bonds

≤ 4

H-donors

0 - 3

H-acceptors

0 - 4

Number of acidic groups

< 2

Number of basic groups

< 2

 No metal or reactive compounds, no undesired chemotypes, no salts are present in the Library, and the PAINS filters were applied. All compounds are available from stock; cherry-picking is available.

Single-fluorine Fragments

Mono-fluorine Subsituted Fragments

Difluoromethyl- and difluoromethylene (CF2) substituted Fragments 

CF2-substituted Fragments

Trifluoromethyl-substituted (CF3) Fragments

CF3-substituted Fragments

Figure 1. Representative compounds from Fluorine Fragment Library

Figure 2. Distribution of differently fluorine-substituted fragments in the Advanced Subset of the Fluorine Fragment Library



Figure 3. Predicted “fragment space” coverage of Life Chemicals fluorinated fragments (in red) is similar to the coverage of >100k commercially available fluorinated fragments from eMolecules (in blue).

References

  1. Jordan J. B. et al. J. Med. Chem. 2012, 55, 678−687.
  2. Vulpetti A, Dalvit C. Drug Discov Today. 2012 Aug;17(15-16):890-7. 
  3. Nagatoishi S, Yamaguchi S et al. Bioorg Med Chem. 2018 May 1;26(8):1929-1938. 
  4. Norton RS, Leung EW et al. Molecules. 2016 Jul 16; 21(7). pii: E860.
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