Screen Fragments

Burrows, J. Lead generation by fragment screening. Presented at SCIpharm 2006 International Pharmaceutical Industry Conference, Edinburgh, 2006. 

Fragment screening by NMR was applied recently in the search of non-peptidic small molecule inhibitors. Two scaffolds (13) and (14), which bind the enzyme at the S1-S3 and the S2 binding site respectively, as shown by chemical shift perturbation, were linked together to yield competitive inhibitors such as (15) with micromolar IC50 values [158]. There have been no reports of non-peptidic inhibitors with potency and pharmacokinetics similar to the peptidic or peptidomimetic inhibitors described above. 

Precursor-ion Scanning Selecting m/z To monitor compounds which in CID give an identical fragment (screening)... 

Dihydroneopterin aldolase (Table 1, entry 8) Inhibitors (such as 33) of dihydro-neopterin aldolase were identified using high throughput X-ray-based fragment screening of a 10,000 member random library [43]. Structure-guided optimisation gave potent leads such as 35. 

Fig. 14.1 Schematic drawing summarizing fragment screening by NMR. Spectra indicated on the left hand side correspond to [ N HJ-HSQC spectra recorded on 15N-labeled protein in the absence (spectrum 1) or presence (spectrum 2) of a first ligand. Cross peaks in the HSQC that have shifted...

DNA gyrase inhibitors from structure-based fragment screening (left, 8 jg/mL) and subsequent lead optimization (right, 0.03 ig/mL)... 

Huang N, Jacobson MP (2010) Binding-site assessment by virtual fragment screening. PloS One 5 el0109... 

Nestler, H. P. (2005) Combinatorial chemistry and fragment screening - Two unlike siblings Curr Drug Diseov Tech 2, 1-12. 

While most pharmaceutical and biotech companies utilize high-throughput screening (HTS) as their primary assay, FBLD offers numerous advantages. Compared with HTS, there is significantly fewer compounds to be screened. There are typically thousands of compounds for a fragment screen versus hundreds... 

Because fragment hits are smaller in size compared with a more drug-like HTS hit, there is much more room for the medicinal chemists to shape them into more novel leads and eventually lead series. This task is made easier if the fragment hits contain chemistry vectors for elaboration, which can be built in when assembling a fragment screening collection. 

Approximately 1,200 amines and 300 carboxylic acids were selected for inclusion in the fragment libraries, from which approximately 20 fragment libraries were synthesized. These libraries yielded 2,000 products with sufficient purity (>95%) and quantity (1.2 mL of 30 xM solution), and the product structures were confirmed via ID NMR. This fragment collection became known as the NMR Combicores to denote their purpose and their combichem origin. It was distributed across several major Pfizer research sites and used in multiple fragment screens. 

There are various methods to conduct a fragment screening campaign. The most commonly utilized methods include various NMR techniques, mass spectrometry, SPR, and biochemical screens. X-ray crystallization is a preferred method since it provides a binding conformation, but can only be used when the target protein is well behaved. Various calorimetry techniques have also been used for fragment screening, but these have been less commonly utilized. The merits of each method have been discussed in the literature (26) and will not be outlined here. 

As mentioned above, all data in the analysis are from fragment screens using NMR spectroscopy to detect fragment binding... 

In recent years there have been encouraging advances in screening technologies suitable for fragment screening. Even for an established method such as NMR, new techniques have been developed and put into practice at various companies that have expanded the scope of targets for FBDD. For example,... 

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